Starting phenix.real_space_refine on Thu Mar 5 14:58:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ddq_30656/03_2026/7ddq_30656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ddq_30656/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ddq_30656/03_2026/7ddq_30656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ddq_30656/03_2026/7ddq_30656.map" model { file = "/net/cci-nas-00/data/ceres_data/7ddq_30656/03_2026/7ddq_30656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ddq_30656/03_2026/7ddq_30656.cif" } 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-5986/lib/python3.9/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: 93 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: 5.24, per 1000 atoms: 0.23 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: 2.06 Conformation dependent library (CDL) restraints added in 760.5 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: 3.24 Time building geometry restraints manager: 2.59 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: 12131 35.99 - 71.98: 339 71.98 - 107.96: 60 107.96 - 143.95: 7 143.95 - 179.94: 31 Dihedral angle restraints: 12568 sinusoidal: 5811 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 12565 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: 1.170 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 20.565 179.938 8204 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 covalent geometry : bond 0.01240 (23465) covalent geometry : angle 1.91574 (32317) hydrogen bonds : bond 0.12958 ( 1309) hydrogen bonds : angle 4.72254 ( 3705) Misc. bond : bond 0.43271 ( 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 : 0.807 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: 0.5529 time to fit residues: 407.6440 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 : 0.792 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3433 r_free = 0.3433 target = 0.084807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065801 restraints weight = 57539.288| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.20 r_work: 0.2824 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23497 Z= 0.170 Angle : 1.406 38.040 32317 Z= 0.516 Chirality : 0.041 0.328 3242 Planarity : 0.004 0.049 3934 Dihedral : 23.073 179.984 3991 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.95 % Allowed : 11.89 % Favored : 85.16 % 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: 1.75 (0.17), residues: 2286 helix: 2.04 (0.13), residues: 1555 sheet: 1.69 (1.08), residues: 22 loop : -0.90 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 53 TYR 0.015 0.002 TYR M 304 PHE 0.039 0.001 PHE M 217 TRP 0.043 0.001 TRP L 273 HIS 0.010 0.001 HIS O 20 Details of bonding type rmsd covalent geometry : bond 0.00388 (23465) covalent geometry : angle 1.40648 (32317) hydrogen bonds : bond 0.05474 ( 1309) hydrogen bonds : angle 4.02868 ( 3705) Misc. bond : bond 0.00114 ( 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: 59 poor density : 550 time to evaluate : 0.795 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: symmetry clash REVERT: o 5 TYR cc_start: 0.8255 (p90) cc_final: 0.7075 (p90) REVERT: N 14 GLN cc_start: 0.9257 (pm20) cc_final: 0.9042 (pm20) REVERT: N 15 GLN cc_start: 0.8789 (pt0) cc_final: 0.8518 (pm20) REVERT: N 18 GLU cc_start: 0.9281 (mp0) cc_final: 0.8998 (pm20) REVERT: t 5 TYR cc_start: 0.8498 (p90) cc_final: 0.8050 (p90) REVERT: t 14 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8511 (mpp80) REVERT: S 19 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9308 (OUTLIER) REVERT: S 27 MET cc_start: 0.9368 (ttm) cc_final: 0.8947 (mtp) REVERT: r 14 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8374 (mpp80) REVERT: r 26 LEU cc_start: 0.9579 (mm) cc_final: 0.9324 (mm) REVERT: r 38 ASN cc_start: 0.9333 (t0) cc_final: 0.9120 (t0) REVERT: U 13 ASP cc_start: 0.9243 (p0) cc_final: 0.8847 (p0) REVERT: b 3 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8773 (mmpt) REVERT: b 30 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8965 (tmm) REVERT: b 45 ASP cc_start: 0.8670 (t0) cc_final: 0.8460 (t0) REVERT: k 5 TYR cc_start: 0.8607 (p90) cc_final: 0.8353 (p90) REVERT: J 11 LEU cc_start: 0.9112 (mp) cc_final: 0.8905 (mp) REVERT: J 18 GLU cc_start: 0.8743 (pp20) cc_final: 0.8506 (pp20) REVERT: J 25 GLN cc_start: 0.9448 (mt0) cc_final: 0.9026 (mm110) REVERT: f 38 ASN cc_start: 0.9208 (t0) cc_final: 0.8986 (t0) REVERT: E 18 GLU cc_start: 0.9035 (mp0) cc_final: 0.8787 (mm-30) REVERT: u 45 ASP cc_start: 0.8651 (m-30) cc_final: 0.8437 (m-30) REVERT: u 53 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7549 (mmt-90) REVERT: T 27 MET cc_start: 0.9007 (ptm) cc_final: 0.8796 (ptp) REVERT: s 6 LYS cc_start: 0.9498 (mmmm) cc_final: 0.9228 (mmmt) REVERT: s 20 GLN cc_start: 0.8692 (mt0) cc_final: 0.8459 (pt0) REVERT: s 25 PHE cc_start: 0.9500 (t80) cc_final: 0.9102 (t80) REVERT: i 3 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8338 (tmmm) REVERT: G 18 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8877 (mt-10) REVERT: j 3 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8612 (ptpp) REVERT: j 26 LEU cc_start: 0.9490 (mt) cc_final: 0.9228 (mm) REVERT: j 45 ASP cc_start: 0.8715 (m-30) cc_final: 0.8415 (m-30) REVERT: I 15 GLN cc_start: 0.8493 (mt0) cc_final: 0.7872 (mt0) REVERT: I 18 GLU cc_start: 0.8409 (pp20) cc_final: 0.8143 (pp20) REVERT: I 19 LEU cc_start: 0.9262 (mp) cc_final: 0.8942 (mp) REVERT: L 217 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.9017 (t80) REVERT: L 272 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8335 (p90) REVERT: g 3 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8712 (tmmm) REVERT: g 38 ASN cc_start: 0.9316 (t0) cc_final: 0.9102 (t0) outliers start: 59 outliers final: 12 residues processed: 565 average time/residue: 0.5289 time to fit residues: 347.6799 Evaluate side-chains 503 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 486 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 D residue 18 GLU 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: 10.0000 chunk 195 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 20 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062811 restraints weight = 58779.206| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.19 r_work: 0.2738 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 23497 Z= 0.239 Angle : 1.352 39.866 32317 Z= 0.501 Chirality : 0.042 0.257 3242 Planarity : 0.004 0.053 3934 Dihedral : 22.563 179.976 3987 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.65 % Allowed : 13.14 % Favored : 83.21 % 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: 1.84 (0.18), residues: 2286 helix: 2.05 (0.13), residues: 1580 sheet: 1.92 (1.10), residues: 26 loop : -0.82 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 45 TYR 0.016 0.002 TYR X 6 PHE 0.029 0.002 PHE M 217 TRP 0.028 0.002 TRP L 273 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00583 (23465) covalent geometry : angle 1.35180 (32317) hydrogen bonds : bond 0.05381 ( 1309) hydrogen bonds : angle 4.00516 ( 3705) Misc. bond : bond 0.00232 ( 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 593 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 520 time to evaluate : 0.875 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: 0.8238 (p90) cc_final: 0.8026 (p90) REVERT: o 6 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9190 (mmpt) REVERT: N 7 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7525 (p) REVERT: N 14 GLN cc_start: 0.9260 (pm20) cc_final: 0.9049 (pm20) REVERT: N 15 GLN cc_start: 0.8799 (pt0) cc_final: 0.8491 (pm20) REVERT: N 18 GLU cc_start: 0.9228 (mp0) cc_final: 0.8935 (pm20) REVERT: t 5 TYR cc_start: 0.8413 (p90) cc_final: 0.8042 (p90) REVERT: t 42 ASN cc_start: 0.8960 (t0) cc_final: 0.8665 (t0) REVERT: S 15 GLN cc_start: 0.8908 (mp10) cc_final: 0.8398 (mp10) REVERT: S 27 MET cc_start: 0.9298 (ttm) cc_final: 0.9060 (mtm) REVERT: r 14 ARG cc_start: 0.8770 (mtm180) cc_final: 0.8434 (mpp80) REVERT: r 23 PHE cc_start: 0.9447 (t80) cc_final: 0.9058 (t80) REVERT: r 38 ASN cc_start: 0.9354 (t0) cc_final: 0.9153 (t0) REVERT: r 46 ILE cc_start: 0.9435 (mt) cc_final: 0.9189 (mp) REVERT: U 13 ASP cc_start: 0.9244 (p0) cc_final: 0.8948 (p0) REVERT: e 38 ASN cc_start: 0.9245 (t0) cc_final: 0.8982 (t0) REVERT: b 3 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8653 (mmpt) REVERT: k 5 TYR cc_start: 0.8568 (p90) cc_final: 0.8305 (p90) REVERT: k 9 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8857 (mm) REVERT: k 14 ARG cc_start: 0.9126 (mtt90) cc_final: 0.8825 (mtt90) REVERT: J 11 LEU cc_start: 0.9191 (mp) cc_final: 0.8949 (mp) REVERT: J 13 ASP cc_start: 0.9517 (t0) cc_final: 0.9157 (t0) REVERT: J 17 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8852 (mp10) REVERT: J 24 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9244 (mm) REVERT: J 25 GLN cc_start: 0.9486 (mt0) cc_final: 0.9112 (mp10) REVERT: f 15 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6292 (ttt-90) REVERT: f 38 ASN cc_start: 0.9256 (t0) cc_final: 0.9041 (t0) REVERT: u 45 ASP cc_start: 0.8640 (m-30) cc_final: 0.8331 (m-30) REVERT: u 53 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7797 (mmt-90) REVERT: T 15 GLN cc_start: 0.8800 (mt0) cc_final: 0.8446 (mt0) REVERT: T 27 MET cc_start: 0.9000 (ptm) cc_final: 0.8743 (ptp) REVERT: s 20 GLN cc_start: 0.8735 (mt0) cc_final: 0.8515 (mt0) REVERT: s 25 PHE cc_start: 0.9520 (t80) cc_final: 0.9080 (t80) REVERT: i 3 LYS cc_start: 0.8707 (tmmm) cc_final: 0.8473 (tmmm) REVERT: G 18 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8885 (mt-10) REVERT: j 26 LEU cc_start: 0.9457 (mt) cc_final: 0.9254 (mm) REVERT: j 42 ASN cc_start: 0.9091 (t0) cc_final: 0.8671 (t0) REVERT: j 45 ASP cc_start: 0.8848 (m-30) cc_final: 0.8233 (m-30) REVERT: I 15 GLN cc_start: 0.8496 (mt0) cc_final: 0.7884 (mt0) REVERT: I 18 GLU cc_start: 0.8510 (pp20) cc_final: 0.8205 (pp20) REVERT: I 19 LEU cc_start: 0.9254 (mp) cc_final: 0.8940 (mp) REVERT: L 272 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8191 (p90) REVERT: g 3 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8750 (tmmm) REVERT: g 38 ASN cc_start: 0.9313 (t0) cc_final: 0.9044 (t0) REVERT: d 12 ASP cc_start: 0.9121 (t0) cc_final: 0.8906 (t0) outliers start: 73 outliers final: 19 residues processed: 548 average time/residue: 0.5437 time to fit residues: 345.5705 Evaluate side-chains 509 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 484 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 24 LEU Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain a residue 37 SER 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 J residue 24 LEU Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain u residue 26 LEU 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 H residue 134 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN ** U 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN b 42 ASN k 42 ASN 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 = 0.3435 r_free = 0.3435 target = 0.084299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065506 restraints weight = 58000.408| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.19 r_work: 0.2820 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23497 Z= 0.145 Angle : 1.250 37.649 32317 Z= 0.466 Chirality : 0.040 0.409 3242 Planarity : 0.003 0.052 3934 Dihedral : 22.296 179.956 3987 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.25 % Allowed : 15.14 % Favored : 81.61 % 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: 2.01 (0.18), residues: 2286 helix: 2.15 (0.13), residues: 1584 sheet: 2.07 (1.09), residues: 26 loop : -0.70 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 45 TYR 0.014 0.001 TYR M 304 PHE 0.017 0.001 PHE f 11 TRP 0.016 0.001 TRP L 273 HIS 0.005 0.001 HIS J 38 Details of bonding type rmsd covalent geometry : bond 0.00342 (23465) covalent geometry : angle 1.25050 (32317) hydrogen bonds : bond 0.04879 ( 1309) hydrogen bonds : angle 3.95180 ( 3705) Misc. bond : bond 0.00114 ( 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 619 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 554 time to evaluate : 0.599 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: 0.8341 (p90) cc_final: 0.8070 (p90) REVERT: o 6 LYS cc_start: 0.9438 (mmtm) cc_final: 0.9191 (mmpt) REVERT: N 7 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7631 (p) REVERT: N 14 GLN cc_start: 0.9190 (pm20) cc_final: 0.8738 (pm20) REVERT: N 15 GLN cc_start: 0.8840 (pt0) cc_final: 0.8218 (pm20) REVERT: N 18 GLU cc_start: 0.9289 (mp0) cc_final: 0.8989 (pm20) REVERT: t 5 TYR cc_start: 0.8398 (p90) cc_final: 0.8174 (p90) REVERT: t 6 LYS cc_start: 0.9400 (mmtp) cc_final: 0.9063 (mmpt) REVERT: t 14 ARG cc_start: 0.8595 (mpp80) cc_final: 0.8189 (mpp80) REVERT: t 42 ASN cc_start: 0.8874 (t0) cc_final: 0.8643 (t0) REVERT: S 15 GLN cc_start: 0.8676 (mp10) cc_final: 0.8379 (mp10) REVERT: r 6 LYS cc_start: 0.9740 (mmmm) cc_final: 0.9497 (mmmt) REVERT: r 14 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8297 (mpp80) REVERT: r 23 PHE cc_start: 0.9416 (t80) cc_final: 0.8894 (t80) REVERT: r 38 ASN cc_start: 0.9397 (t0) cc_final: 0.9195 (t0) REVERT: r 46 ILE cc_start: 0.9481 (mt) cc_final: 0.9238 (mp) REVERT: e 20 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8956 (tt0) REVERT: e 38 ASN cc_start: 0.9303 (t0) cc_final: 0.9085 (t0) REVERT: b 30 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8855 (tpt) REVERT: k 9 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8896 (mm) REVERT: k 42 ASN cc_start: 0.8924 (t0) cc_final: 0.8693 (t0) REVERT: k 45 ASP cc_start: 0.8851 (m-30) cc_final: 0.8616 (m-30) REVERT: J 11 LEU cc_start: 0.9126 (mp) cc_final: 0.8803 (mp) REVERT: J 25 GLN cc_start: 0.9491 (mt0) cc_final: 0.9114 (mp10) REVERT: f 38 ASN cc_start: 0.9293 (t0) cc_final: 0.9074 (t0) REVERT: E 14 GLN cc_start: 0.8753 (pm20) cc_final: 0.8515 (pm20) REVERT: E 18 GLU cc_start: 0.9004 (mp0) cc_final: 0.8749 (mm-30) REVERT: u 30 MET cc_start: 0.8788 (tpp) cc_final: 0.8544 (ttp) REVERT: u 45 ASP cc_start: 0.8647 (m-30) cc_final: 0.8324 (m-30) REVERT: T 15 GLN cc_start: 0.8794 (mt0) cc_final: 0.8444 (mt0) REVERT: T 27 MET cc_start: 0.9004 (ptm) cc_final: 0.8782 (ptp) REVERT: s 20 GLN cc_start: 0.8753 (mt0) cc_final: 0.8497 (pt0) REVERT: s 25 PHE cc_start: 0.9492 (t80) cc_final: 0.8990 (t80) REVERT: R 27 MET cc_start: 0.8752 (ttp) cc_final: 0.8316 (ttm) REVERT: K 14 GLN cc_start: 0.8706 (pm20) cc_final: 0.8472 (pm20) REVERT: K 15 GLN cc_start: 0.9051 (mt0) cc_final: 0.8758 (mp10) REVERT: i 3 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8438 (tmmm) REVERT: G 14 GLN cc_start: 0.9023 (pm20) cc_final: 0.8816 (pm20) REVERT: G 15 GLN cc_start: 0.8966 (mt0) cc_final: 0.8729 (mt0) REVERT: G 18 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8824 (mt-10) REVERT: j 42 ASN cc_start: 0.9151 (t0) cc_final: 0.8653 (t0) REVERT: j 45 ASP cc_start: 0.8814 (m-30) cc_final: 0.8126 (m-30) REVERT: I 15 GLN cc_start: 0.8596 (mt0) cc_final: 0.7913 (mt0) REVERT: I 18 GLU cc_start: 0.8486 (pp20) cc_final: 0.8153 (pp20) REVERT: I 19 LEU cc_start: 0.9297 (mp) cc_final: 0.8930 (mp) REVERT: L 149 TYR cc_start: 0.9168 (m-80) cc_final: 0.8764 (m-80) REVERT: L 272 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8069 (p90) REVERT: H 206 GLN cc_start: 0.9046 (mt0) cc_final: 0.8725 (pt0) REVERT: g 3 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8766 (tmmm) REVERT: g 38 ASN cc_start: 0.9346 (t0) cc_final: 0.9080 (t0) REVERT: F 48 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8626 (mt) outliers start: 65 outliers final: 18 residues processed: 579 average time/residue: 0.5216 time to fit residues: 351.2703 Evaluate side-chains 520 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 494 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 24 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain e residue 20 GLN Chi-restraints excluded: chain b residue 30 MET Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain u residue 54 VAL 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 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 M residue 230 LEU Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain g residue 34 MET 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: 0.9980 chunk 190 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN o 38 ASN t 20 GLN b 42 ASN ** f 20 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.082154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.063271 restraints weight = 58219.144| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.18 r_work: 0.2769 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2996 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= 0.222 Angle : 1.256 38.318 32317 Z= 0.475 Chirality : 0.042 0.344 3242 Planarity : 0.004 0.054 3934 Dihedral : 22.138 179.984 3985 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.40 % Allowed : 15.09 % Favored : 81.51 % 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: 2.10 (0.13), residues: 1581 sheet: 2.15 (1.08), residues: 26 loop : -0.77 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 45 TYR 0.013 0.001 TYR M 304 PHE 0.019 0.001 PHE H 20 TRP 0.017 0.001 TRP L 273 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00546 (23465) covalent geometry : angle 1.25585 (32317) hydrogen bonds : bond 0.05143 ( 1309) hydrogen bonds : angle 4.02243 ( 3705) Misc. bond : bond 0.00183 ( 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 582 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 514 time to evaluate : 0.858 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: 0.8394 (p90) cc_final: 0.7595 (p90) REVERT: o 6 LYS cc_start: 0.9444 (mmtm) cc_final: 0.9127 (mmpt) REVERT: o 34 MET cc_start: 0.9213 (ptp) cc_final: 0.8900 (ptm) REVERT: N 7 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7658 (p) REVERT: N 14 GLN cc_start: 0.9221 (pm20) cc_final: 0.8976 (pm20) REVERT: N 15 GLN cc_start: 0.8860 (pt0) cc_final: 0.8433 (pm20) REVERT: N 18 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9073 (pt0) REVERT: t 6 LYS cc_start: 0.9417 (mmtp) cc_final: 0.9126 (mmpt) REVERT: t 14 ARG cc_start: 0.8696 (mpp80) cc_final: 0.8271 (mpp80) REVERT: t 42 ASN cc_start: 0.8886 (t0) cc_final: 0.8630 (t0) REVERT: t 45 ASP cc_start: 0.8889 (t0) cc_final: 0.8548 (t0) REVERT: S 15 GLN cc_start: 0.8535 (mp10) cc_final: 0.8254 (mp10) REVERT: S 18 GLU cc_start: 0.9271 (mp0) cc_final: 0.9010 (pm20) REVERT: S 19 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9255 (tp) REVERT: S 27 MET cc_start: 0.9360 (ttm) cc_final: 0.9089 (mtm) REVERT: r 6 LYS cc_start: 0.9717 (mmmm) cc_final: 0.9506 (mmpt) REVERT: r 14 ARG cc_start: 0.8775 (mtm180) cc_final: 0.8373 (mpp80) REVERT: r 23 PHE cc_start: 0.9401 (t80) cc_final: 0.8910 (t80) REVERT: r 38 ASN cc_start: 0.9410 (t0) cc_final: 0.9203 (t0) REVERT: r 46 ILE cc_start: 0.9480 (mt) cc_final: 0.9236 (mp) REVERT: k 9 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8984 (mm) REVERT: J 11 LEU cc_start: 0.9141 (mp) cc_final: 0.8770 (mp) REVERT: J 24 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9110 (mm) REVERT: J 25 GLN cc_start: 0.9501 (mt0) cc_final: 0.9067 (mp10) REVERT: f 15 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5752 (ttp-110) REVERT: f 38 ASN cc_start: 0.9306 (t0) cc_final: 0.9072 (t0) REVERT: E 14 GLN cc_start: 0.8842 (pm20) cc_final: 0.8569 (pm20) REVERT: E 18 GLU cc_start: 0.9084 (mp0) cc_final: 0.8800 (mm-30) REVERT: u 45 ASP cc_start: 0.8639 (m-30) cc_final: 0.8290 (m-30) REVERT: T 15 GLN cc_start: 0.8775 (mt0) cc_final: 0.8447 (mt0) REVERT: T 27 MET cc_start: 0.9036 (ptm) cc_final: 0.8778 (ptp) REVERT: X 15 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8452 (mtt) REVERT: s 20 GLN cc_start: 0.8755 (mt0) cc_final: 0.8547 (pt0) REVERT: s 25 PHE cc_start: 0.9492 (t80) cc_final: 0.9048 (t80) REVERT: R 27 MET cc_start: 0.8812 (ttp) cc_final: 0.8409 (ttm) REVERT: K 14 GLN cc_start: 0.8882 (pm20) cc_final: 0.8631 (pm20) REVERT: K 15 GLN cc_start: 0.9077 (mt0) cc_final: 0.8739 (mp10) REVERT: i 3 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (tmmm) REVERT: G 14 GLN cc_start: 0.9079 (pm20) cc_final: 0.8877 (pm20) REVERT: G 15 GLN cc_start: 0.8951 (mt0) cc_final: 0.8677 (mt0) REVERT: G 18 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8920 (mt-10) REVERT: j 42 ASN cc_start: 0.9171 (t0) cc_final: 0.8528 (t0) REVERT: j 45 ASP cc_start: 0.8841 (m-30) cc_final: 0.8131 (m-30) REVERT: I 15 GLN cc_start: 0.8656 (mt0) cc_final: 0.7938 (mt0) REVERT: I 18 GLU cc_start: 0.8514 (pp20) cc_final: 0.8200 (pp20) REVERT: I 19 LEU cc_start: 0.9294 (mp) cc_final: 0.8898 (mp) REVERT: L 272 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7954 (p90) REVERT: H 206 GLN cc_start: 0.9115 (mt0) cc_final: 0.8841 (pt0) REVERT: g 38 ASN cc_start: 0.9336 (t0) cc_final: 0.9013 (t0) REVERT: F 48 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8657 (mt) REVERT: d 38 ASN cc_start: 0.9426 (t0) cc_final: 0.9222 (t0) outliers start: 68 outliers final: 21 residues processed: 544 average time/residue: 0.5416 time to fit residues: 341.8780 Evaluate side-chains 505 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 475 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain r residue 34 MET Chi-restraints excluded: chain a residue 37 SER 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 J residue 24 LEU Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 15 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 L residue 82 ARG 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 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: 0.9990 chunk 220 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 153 optimal weight: 0.0570 chunk 218 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN e 20 GLN b 42 ASN k 42 ASN ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN M 78 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064939 restraints weight = 58170.989| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.19 r_work: 0.2814 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3197 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= 0.157 Angle : 1.193 37.863 32317 Z= 0.457 Chirality : 0.042 0.385 3242 Planarity : 0.003 0.053 3934 Dihedral : 21.978 179.991 3985 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.25 % Allowed : 16.09 % Favored : 80.66 % 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: 1.98 (0.18), residues: 2286 helix: 2.12 (0.13), residues: 1584 sheet: 2.14 (1.07), residues: 26 loop : -0.69 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 45 TYR 0.019 0.001 TYR M 304 PHE 0.016 0.001 PHE H 20 TRP 0.014 0.001 TRP k 43 HIS 0.005 0.001 HIS I 20 Details of bonding type rmsd covalent geometry : bond 0.00380 (23465) covalent geometry : angle 1.19276 (32317) hydrogen bonds : bond 0.04842 ( 1309) hydrogen bonds : angle 4.02281 ( 3705) Misc. bond : bond 0.00114 ( 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 592 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 527 time to evaluate : 0.808 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: 0.8330 (p90) cc_final: 0.7900 (p90) REVERT: o 6 LYS cc_start: 0.9431 (mmtm) cc_final: 0.9170 (mmpt) REVERT: N 7 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7692 (p) REVERT: N 14 GLN cc_start: 0.9198 (pm20) cc_final: 0.8941 (pm20) REVERT: N 15 GLN cc_start: 0.8841 (pt0) cc_final: 0.8367 (pm20) REVERT: N 18 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9039 (pt0) REVERT: t 6 LYS cc_start: 0.9392 (mmtp) cc_final: 0.9128 (mmpt) REVERT: t 14 ARG cc_start: 0.8668 (mpp80) cc_final: 0.8253 (mpp80) REVERT: t 45 ASP cc_start: 0.8869 (t0) cc_final: 0.8592 (t0) REVERT: S 15 GLN cc_start: 0.8490 (mp10) cc_final: 0.8229 (mp10) REVERT: S 18 GLU cc_start: 0.9202 (mp0) cc_final: 0.8957 (pm20) REVERT: S 19 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9270 (tp) REVERT: S 27 MET cc_start: 0.9361 (ttm) cc_final: 0.9117 (mtp) REVERT: r 14 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8308 (mpp80) REVERT: r 23 PHE cc_start: 0.9374 (t80) cc_final: 0.8929 (t80) REVERT: r 26 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9363 (mm) REVERT: r 38 ASN cc_start: 0.9405 (t0) cc_final: 0.9197 (t0) REVERT: r 46 ILE cc_start: 0.9482 (mt) cc_final: 0.9234 (mp) REVERT: k 9 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9007 (mm) REVERT: k 42 ASN cc_start: 0.8942 (t0) cc_final: 0.8612 (t0) REVERT: k 45 ASP cc_start: 0.8782 (m-30) cc_final: 0.8481 (m-30) REVERT: J 24 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8999 (mm) REVERT: J 25 GLN cc_start: 0.9486 (mt0) cc_final: 0.9034 (mp10) REVERT: f 38 ASN cc_start: 0.9299 (t0) cc_final: 0.9065 (t0) REVERT: E 14 GLN cc_start: 0.8877 (pm20) cc_final: 0.8534 (pm20) REVERT: E 18 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8801 (mm-30) REVERT: u 45 ASP cc_start: 0.8599 (m-30) cc_final: 0.8252 (m-30) REVERT: T 15 GLN cc_start: 0.8790 (mt0) cc_final: 0.8449 (mt0) REVERT: X 15 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: s 25 PHE cc_start: 0.9472 (t80) cc_final: 0.9067 (t80) REVERT: n 5 TYR cc_start: 0.8123 (p90) cc_final: 0.7800 (p90) REVERT: K 14 GLN cc_start: 0.8916 (pm20) cc_final: 0.8606 (pm20) REVERT: K 15 GLN cc_start: 0.9131 (mt0) cc_final: 0.8802 (mp10) REVERT: i 6 LYS cc_start: 0.9377 (tppt) cc_final: 0.9120 (tptp) REVERT: G 14 GLN cc_start: 0.9076 (pm20) cc_final: 0.8842 (pm20) REVERT: G 15 GLN cc_start: 0.8950 (mt0) cc_final: 0.8640 (mt0) REVERT: G 18 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8851 (mt-10) REVERT: j 42 ASN cc_start: 0.9208 (t0) cc_final: 0.8485 (t0) REVERT: j 45 ASP cc_start: 0.8855 (m-30) cc_final: 0.8383 (m-30) REVERT: I 15 GLN cc_start: 0.8644 (mt0) cc_final: 0.7885 (mt0) REVERT: I 18 GLU cc_start: 0.8458 (pp20) cc_final: 0.8035 (pp20) REVERT: I 19 LEU cc_start: 0.9301 (mp) cc_final: 0.8902 (mp) REVERT: L 272 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7943 (p90) REVERT: H 206 GLN cc_start: 0.9005 (mt0) cc_final: 0.8727 (pt0) REVERT: g 3 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8270 (tmmm) REVERT: g 38 ASN cc_start: 0.9343 (t0) cc_final: 0.9018 (t0) REVERT: d 38 ASN cc_start: 0.9434 (t0) cc_final: 0.9220 (t0) outliers start: 65 outliers final: 23 residues processed: 555 average time/residue: 0.5293 time to fit residues: 342.0414 Evaluate side-chains 524 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 492 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 24 LEU 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 34 MET 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 k residue 9 LEU Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain u residue 54 VAL Chi-restraints excluded: chain X residue 15 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 96 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 120 optimal weight: 50.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN e 20 GLN b 42 ASN A 25 GLN ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN L 61 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 = 0.3407 r_free = 0.3407 target = 0.082745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063946 restraints weight = 58539.666| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.18 r_work: 0.2790 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23497 Z= 0.202 Angle : 1.162 38.115 32317 Z= 0.457 Chirality : 0.042 0.431 3242 Planarity : 0.004 0.054 3934 Dihedral : 21.918 179.984 3985 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.40 % Allowed : 17.24 % Favored : 79.36 % 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: 1.86 (0.18), residues: 2286 helix: 2.05 (0.13), residues: 1583 sheet: 1.71 (1.39), residues: 16 loop : -0.73 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 45 TYR 0.028 0.001 TYR M 304 PHE 0.017 0.001 PHE H 20 TRP 0.015 0.001 TRP e 43 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00494 (23465) covalent geometry : angle 1.16189 (32317) hydrogen bonds : bond 0.05031 ( 1309) hydrogen bonds : angle 4.14823 ( 3705) Misc. bond : bond 0.00164 ( 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 581 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 513 time to evaluate : 0.889 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: 0.8327 (p90) cc_final: 0.7629 (p90) REVERT: o 6 LYS cc_start: 0.9387 (mmtm) cc_final: 0.9143 (mmpt) REVERT: N 7 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7689 (p) REVERT: N 14 GLN cc_start: 0.9191 (pm20) cc_final: 0.8941 (pm20) REVERT: N 15 GLN cc_start: 0.8827 (pt0) cc_final: 0.8321 (pm20) REVERT: N 18 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9043 (pt0) REVERT: t 6 LYS cc_start: 0.9391 (mmtp) cc_final: 0.9086 (mmtt) REVERT: t 14 ARG cc_start: 0.8677 (mpp80) cc_final: 0.8245 (mpp80) REVERT: t 45 ASP cc_start: 0.8839 (t0) cc_final: 0.8576 (t0) REVERT: S 15 GLN cc_start: 0.8483 (mp10) cc_final: 0.8240 (mp10) REVERT: S 18 GLU cc_start: 0.9202 (mp0) cc_final: 0.8947 (pm20) REVERT: S 19 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9272 (tp) REVERT: S 27 MET cc_start: 0.9269 (ttm) cc_final: 0.8974 (mtm) REVERT: r 14 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8166 (mpp80) REVERT: r 23 PHE cc_start: 0.9372 (t80) cc_final: 0.8951 (t80) REVERT: r 26 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9386 (mm) REVERT: r 38 ASN cc_start: 0.9416 (t0) cc_final: 0.9201 (t0) REVERT: r 46 ILE cc_start: 0.9484 (mt) cc_final: 0.9234 (mp) REVERT: k 14 ARG cc_start: 0.9204 (mtt90) cc_final: 0.8888 (mtt90) REVERT: J 24 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8935 (mm) REVERT: J 25 GLN cc_start: 0.9477 (mt0) cc_final: 0.8999 (mp10) REVERT: f 15 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6654 (ttt-90) REVERT: f 38 ASN cc_start: 0.9289 (t0) cc_final: 0.9063 (t0) REVERT: E 14 GLN cc_start: 0.8905 (pm20) cc_final: 0.8589 (pm20) REVERT: E 18 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8890 (mm-30) REVERT: u 53 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7484 (mpp-170) REVERT: T 15 GLN cc_start: 0.8774 (mt0) cc_final: 0.8501 (mt0) REVERT: X 12 LYS cc_start: 0.8303 (tppt) cc_final: 0.8067 (tppt) REVERT: X 15 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8445 (mtt) REVERT: s 25 PHE cc_start: 0.9483 (t80) cc_final: 0.9081 (t80) REVERT: R 19 LEU cc_start: 0.9529 (tt) cc_final: 0.9267 (pp) REVERT: R 27 MET cc_start: 0.8856 (ttp) cc_final: 0.8628 (ttp) REVERT: n 5 TYR cc_start: 0.8166 (p90) cc_final: 0.7855 (p90) REVERT: K 14 GLN cc_start: 0.8939 (pm20) cc_final: 0.8716 (pm20) REVERT: K 15 GLN cc_start: 0.9126 (mt0) cc_final: 0.8638 (pm20) REVERT: i 3 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8153 (tmmm) REVERT: G 14 GLN cc_start: 0.9090 (pm20) cc_final: 0.8858 (pm20) REVERT: G 15 GLN cc_start: 0.8947 (mt0) cc_final: 0.8637 (mt0) REVERT: G 18 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8876 (mt-10) REVERT: j 42 ASN cc_start: 0.9252 (t0) cc_final: 0.8413 (t0) REVERT: j 45 ASP cc_start: 0.8846 (m-30) cc_final: 0.8309 (m-30) REVERT: I 15 GLN cc_start: 0.8657 (mt0) cc_final: 0.7912 (mt0) REVERT: I 18 GLU cc_start: 0.8471 (pp20) cc_final: 0.8169 (pp20) REVERT: I 19 LEU cc_start: 0.9296 (mp) cc_final: 0.8900 (mp) REVERT: L 272 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8066 (p90) REVERT: H 206 GLN cc_start: 0.9063 (mt0) cc_final: 0.8840 (pt0) REVERT: g 3 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8658 (tmmm) REVERT: g 38 ASN cc_start: 0.9361 (t0) cc_final: 0.9000 (t0) REVERT: d 38 ASN cc_start: 0.9450 (t0) cc_final: 0.9215 (t0) outliers start: 68 outliers final: 31 residues processed: 545 average time/residue: 0.5478 time to fit residues: 345.4354 Evaluate side-chains 526 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 485 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 24 LEU 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 34 MET 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 J residue 24 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 20 GLN 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 15 MET Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain n residue 10 ILE 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 G residue 11 LEU Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain L residue 207 MET 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: 0.8980 chunk 123 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 218 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065515 restraints weight = 57765.447| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.18 r_work: 0.2834 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23497 Z= 0.157 Angle : 1.153 38.315 32317 Z= 0.459 Chirality : 0.042 0.414 3242 Planarity : 0.003 0.053 3934 Dihedral : 21.798 179.990 3985 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.55 % Allowed : 19.64 % Favored : 77.81 % 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: 1.85 (0.18), residues: 2286 helix: 2.02 (0.13), residues: 1585 sheet: 1.85 (1.40), residues: 16 loop : -0.67 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 45 TYR 0.029 0.001 TYR M 304 PHE 0.016 0.001 PHE H 20 TRP 0.014 0.001 TRP k 43 HIS 0.005 0.001 HIS X 5 Details of bonding type rmsd covalent geometry : bond 0.00383 (23465) covalent geometry : angle 1.15316 (32317) hydrogen bonds : bond 0.04825 ( 1309) hydrogen bonds : angle 4.20528 ( 3705) Misc. bond : bond 0.00092 ( 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 574 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 523 time to evaluate : 0.751 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: 0.8358 (p90) cc_final: 0.7721 (p90) REVERT: o 6 LYS cc_start: 0.9359 (mmtm) cc_final: 0.8968 (tppt) REVERT: N 15 GLN cc_start: 0.8823 (pt0) cc_final: 0.8368 (pm20) REVERT: N 18 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9042 (pt0) REVERT: t 5 TYR cc_start: 0.8345 (p90) cc_final: 0.8003 (p90) REVERT: t 14 ARG cc_start: 0.8692 (mpp80) cc_final: 0.8257 (mpp80) REVERT: t 33 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9339 (mm) REVERT: t 45 ASP cc_start: 0.8792 (t0) cc_final: 0.8514 (t0) REVERT: S 15 GLN cc_start: 0.8570 (mp10) cc_final: 0.8291 (mp10) REVERT: S 18 GLU cc_start: 0.9204 (mp0) cc_final: 0.8940 (pm20) REVERT: S 27 MET cc_start: 0.9264 (ttm) cc_final: 0.8956 (mtp) REVERT: r 14 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8269 (mpp80) REVERT: r 23 PHE cc_start: 0.9318 (t80) cc_final: 0.8952 (t80) REVERT: r 26 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9370 (mm) REVERT: r 38 ASN cc_start: 0.9405 (t0) cc_final: 0.9178 (t0) REVERT: r 46 ILE cc_start: 0.9497 (mt) cc_final: 0.9260 (mp) REVERT: O 18 GLU cc_start: 0.9291 (pt0) cc_final: 0.9071 (pt0) REVERT: U 44 TRP cc_start: 0.8498 (t60) cc_final: 0.8235 (t60) REVERT: k 14 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8893 (mtt90) REVERT: J 24 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8913 (mm) REVERT: J 25 GLN cc_start: 0.9463 (mt0) cc_final: 0.8970 (mp10) REVERT: f 38 ASN cc_start: 0.9295 (t0) cc_final: 0.9042 (t0) REVERT: E 14 GLN cc_start: 0.8899 (pm20) cc_final: 0.8552 (pm20) REVERT: E 18 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8876 (mm-30) REVERT: u 20 GLN cc_start: 0.9074 (mt0) cc_final: 0.8812 (mt0) REVERT: u 53 ARG cc_start: 0.7994 (mmt-90) cc_final: 0.7163 (mmp80) REVERT: T 15 GLN cc_start: 0.8755 (mt0) cc_final: 0.8501 (mt0) REVERT: s 25 PHE cc_start: 0.9438 (t80) cc_final: 0.9110 (t80) REVERT: R 19 LEU cc_start: 0.9538 (tt) cc_final: 0.9264 (pp) REVERT: R 27 MET cc_start: 0.8813 (ttp) cc_final: 0.8560 (ttp) REVERT: n 5 TYR cc_start: 0.8146 (p90) cc_final: 0.7751 (p90) REVERT: K 15 GLN cc_start: 0.9090 (mt0) cc_final: 0.8533 (mp10) REVERT: K 18 GLU cc_start: 0.9048 (pm20) cc_final: 0.8843 (pm20) REVERT: i 3 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8135 (tmmm) REVERT: i 6 LYS cc_start: 0.9385 (tppp) cc_final: 0.8999 (tppt) REVERT: G 14 GLN cc_start: 0.9106 (pm20) cc_final: 0.8876 (pm20) REVERT: G 15 GLN cc_start: 0.8961 (mt0) cc_final: 0.8617 (mt0) REVERT: G 18 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8817 (mt-10) REVERT: j 3 LYS cc_start: 0.9097 (mmpt) cc_final: 0.8843 (ptpp) REVERT: j 42 ASN cc_start: 0.9250 (t0) cc_final: 0.8409 (t0) REVERT: j 45 ASP cc_start: 0.8803 (m-30) cc_final: 0.8279 (m-30) REVERT: I 15 GLN cc_start: 0.8694 (mt0) cc_final: 0.7926 (mt0) REVERT: I 18 GLU cc_start: 0.8518 (pp20) cc_final: 0.8213 (pp20) REVERT: I 19 LEU cc_start: 0.9287 (mp) cc_final: 0.8895 (mp) REVERT: L 149 TYR cc_start: 0.9197 (m-80) cc_final: 0.8861 (m-80) REVERT: L 272 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7974 (p90) REVERT: H 206 GLN cc_start: 0.8958 (mt0) cc_final: 0.8717 (pt0) REVERT: g 3 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8652 (tmmm) REVERT: g 38 ASN cc_start: 0.9367 (t0) cc_final: 0.9000 (t0) REVERT: d 38 ASN cc_start: 0.9469 (t0) cc_final: 0.9231 (t0) outliers start: 51 outliers final: 26 residues processed: 551 average time/residue: 0.5183 time to fit residues: 332.7943 Evaluate side-chains 527 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 494 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 31 ILE 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 J residue 24 LEU 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 n residue 10 ILE 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 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 29 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN e 20 GLN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN L 61 ASN M 78 GLN H 93 ASN g 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.063467 restraints weight = 58458.002| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.20 r_work: 0.2765 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 23497 Z= 0.225 Angle : 1.192 38.194 32317 Z= 0.479 Chirality : 0.045 0.418 3242 Planarity : 0.004 0.054 3934 Dihedral : 21.780 179.999 3985 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.60 % Allowed : 20.69 % Favored : 76.71 % 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: 1.74 (0.18), residues: 2286 helix: 1.94 (0.13), residues: 1584 sheet: 1.59 (1.43), residues: 16 loop : -0.74 (0.24), residues: 686 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 0.015 0.001 TRP e 43 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00553 (23465) covalent geometry : angle 1.19169 (32317) hydrogen bonds : bond 0.05094 ( 1309) hydrogen bonds : angle 4.27819 ( 3705) Misc. bond : bond 0.00190 ( 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 555 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 503 time to evaluate : 0.838 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: 0.8385 (p90) cc_final: 0.8096 (p90) REVERT: o 6 LYS cc_start: 0.9475 (mmtm) cc_final: 0.9115 (tppt) REVERT: N 15 GLN cc_start: 0.8784 (pt0) cc_final: 0.8358 (pm20) REVERT: N 18 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9023 (pt0) REVERT: t 5 TYR cc_start: 0.8374 (p90) cc_final: 0.7977 (p90) REVERT: t 6 LYS cc_start: 0.9335 (mmtp) cc_final: 0.9029 (mmpt) REVERT: t 14 ARG cc_start: 0.8696 (mpp80) cc_final: 0.8236 (mpp80) REVERT: t 33 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9305 (mm) REVERT: t 45 ASP cc_start: 0.8837 (t0) cc_final: 0.8552 (t0) REVERT: S 15 GLN cc_start: 0.8686 (mp10) cc_final: 0.8287 (mp10) REVERT: S 18 GLU cc_start: 0.9179 (mp0) cc_final: 0.8937 (pm20) REVERT: S 27 MET cc_start: 0.9272 (ttm) cc_final: 0.8948 (mtp) REVERT: r 14 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8192 (mpp80) REVERT: r 23 PHE cc_start: 0.9314 (t80) cc_final: 0.8909 (t80) REVERT: r 26 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9345 (mm) REVERT: r 46 ILE cc_start: 0.9466 (mt) cc_final: 0.9212 (mp) REVERT: O 18 GLU cc_start: 0.9330 (pt0) cc_final: 0.9114 (pt0) REVERT: U 44 TRP cc_start: 0.8466 (t60) cc_final: 0.8221 (t60) REVERT: k 9 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8963 (mm) REVERT: k 14 ARG cc_start: 0.9135 (mtt90) cc_final: 0.8814 (mtt90) REVERT: k 42 ASN cc_start: 0.8965 (t0) cc_final: 0.8564 (t0) REVERT: J 24 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8935 (mm) REVERT: J 25 GLN cc_start: 0.9464 (mt0) cc_final: 0.8938 (mp10) REVERT: f 38 ASN cc_start: 0.9279 (t0) cc_final: 0.9017 (t0) REVERT: E 14 GLN cc_start: 0.8966 (pm20) cc_final: 0.8627 (pm20) REVERT: E 18 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8860 (mm-30) REVERT: u 53 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7509 (mpp-170) REVERT: X 63 THR cc_start: 0.8828 (m) cc_final: 0.8587 (p) REVERT: s 25 PHE cc_start: 0.9452 (t80) cc_final: 0.9096 (t80) REVERT: R 27 MET cc_start: 0.8818 (ttp) cc_final: 0.8571 (mtp) REVERT: n 5 TYR cc_start: 0.8190 (p90) cc_final: 0.7836 (p90) REVERT: K 15 GLN cc_start: 0.9135 (mt0) cc_final: 0.8425 (mp10) REVERT: i 3 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8257 (tmmm) REVERT: i 6 LYS cc_start: 0.9425 (tppp) cc_final: 0.9096 (tppt) REVERT: G 14 GLN cc_start: 0.9110 (pm20) cc_final: 0.8851 (pm20) REVERT: G 15 GLN cc_start: 0.8934 (mt0) cc_final: 0.8557 (mt0) REVERT: G 18 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8897 (mt-10) REVERT: j 42 ASN cc_start: 0.9275 (t0) cc_final: 0.8462 (t0) REVERT: j 45 ASP cc_start: 0.8831 (m-30) cc_final: 0.8279 (m-30) REVERT: I 15 GLN cc_start: 0.8645 (mt0) cc_final: 0.7911 (mt0) REVERT: I 18 GLU cc_start: 0.8533 (pp20) cc_final: 0.8247 (pp20) REVERT: I 19 LEU cc_start: 0.9265 (mp) cc_final: 0.8894 (mp) REVERT: L 272 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8168 (p90) REVERT: H 93 ASN cc_start: 0.8414 (t0) cc_final: 0.8073 (t0) REVERT: H 206 GLN cc_start: 0.9067 (mt0) cc_final: 0.8844 (pt0) REVERT: g 3 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8705 (tmmm) REVERT: g 38 ASN cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: d 38 ASN cc_start: 0.9438 (t0) cc_final: 0.9187 (t0) outliers start: 52 outliers final: 27 residues processed: 528 average time/residue: 0.5366 time to fit residues: 328.6701 Evaluate side-chains 520 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 485 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain U residue 31 ILE 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 J residue 24 LEU 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 15 GLN Chi-restraints excluded: chain R residue 24 LEU 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 207 MET 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 g residue 20 GLN 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: 1.9990 chunk 198 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN e 20 GLN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN M 78 GLN g 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064093 restraints weight = 58465.372| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.20 r_work: 0.2783 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23497 Z= 0.187 Angle : 1.190 38.184 32317 Z= 0.482 Chirality : 0.044 0.436 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.773 179.982 3985 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.15 % Allowed : 21.49 % Favored : 76.36 % 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: 1.72 (0.18), residues: 2286 helix: 1.91 (0.13), residues: 1584 sheet: 1.58 (1.43), residues: 16 loop : -0.70 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG U 45 TYR 0.030 0.001 TYR M 304 PHE 0.017 0.001 PHE H 20 TRP 0.014 0.001 TRP k 43 HIS 0.005 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00462 (23465) covalent geometry : angle 1.18971 (32317) hydrogen bonds : bond 0.05030 ( 1309) hydrogen bonds : angle 4.30602 ( 3705) Misc. bond : bond 0.00136 ( 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 549 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 506 time to evaluate : 0.780 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: 0.8540 (p90) cc_final: 0.8043 (p90) REVERT: o 6 LYS cc_start: 0.9444 (mmtm) cc_final: 0.9120 (mmmt) REVERT: N 15 GLN cc_start: 0.8767 (pt0) cc_final: 0.8342 (pm20) REVERT: N 18 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9055 (pt0) REVERT: t 5 TYR cc_start: 0.8391 (p90) cc_final: 0.7994 (p90) REVERT: t 6 LYS cc_start: 0.9328 (mmtp) cc_final: 0.9021 (mmpt) REVERT: t 14 ARG cc_start: 0.8667 (mpp80) cc_final: 0.8206 (mpp80) REVERT: t 33 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9294 (mm) REVERT: t 45 ASP cc_start: 0.8827 (t0) cc_final: 0.8544 (t0) REVERT: S 11 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8348 (tt) REVERT: S 15 GLN cc_start: 0.8706 (mp10) cc_final: 0.8316 (mp10) REVERT: S 18 GLU cc_start: 0.9168 (mp0) cc_final: 0.8937 (pm20) REVERT: S 27 MET cc_start: 0.9232 (ttm) cc_final: 0.8909 (mtm) REVERT: r 14 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8297 (mpp80) REVERT: r 23 PHE cc_start: 0.9298 (t80) cc_final: 0.8950 (t80) REVERT: r 26 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9357 (mm) REVERT: r 46 ILE cc_start: 0.9469 (mt) cc_final: 0.9239 (mp) REVERT: O 18 GLU cc_start: 0.9337 (pt0) cc_final: 0.9106 (pt0) REVERT: U 44 TRP cc_start: 0.8498 (t60) cc_final: 0.8254 (t60) REVERT: k 9 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8996 (mm) REVERT: k 14 ARG cc_start: 0.9139 (mtt90) cc_final: 0.8826 (mtt90) REVERT: k 42 ASN cc_start: 0.8990 (t0) cc_final: 0.8585 (t0) REVERT: J 24 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8887 (mm) REVERT: J 25 GLN cc_start: 0.9471 (mt0) cc_final: 0.8933 (mp10) REVERT: f 38 ASN cc_start: 0.9275 (t0) cc_final: 0.9013 (t0) REVERT: E 14 GLN cc_start: 0.8969 (pm20) cc_final: 0.8629 (pm20) REVERT: E 18 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8890 (mm-30) REVERT: u 53 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7533 (mpp-170) REVERT: X 63 THR cc_start: 0.8821 (m) cc_final: 0.8592 (p) REVERT: s 25 PHE cc_start: 0.9440 (t80) cc_final: 0.9123 (t80) REVERT: s 42 ASN cc_start: 0.9070 (t0) cc_final: 0.8826 (t0) REVERT: s 45 ASP cc_start: 0.8957 (m-30) cc_final: 0.8431 (m-30) REVERT: R 27 MET cc_start: 0.8805 (ttp) cc_final: 0.8578 (mtp) REVERT: n 5 TYR cc_start: 0.8155 (p90) cc_final: 0.7768 (p90) REVERT: K 15 GLN cc_start: 0.8874 (mt0) cc_final: 0.8478 (pm20) REVERT: G 14 GLN cc_start: 0.9103 (pm20) cc_final: 0.8878 (pm20) REVERT: G 15 GLN cc_start: 0.8920 (mt0) cc_final: 0.8547 (mt0) REVERT: G 18 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8850 (mt-10) REVERT: j 3 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8775 (ptpp) REVERT: j 42 ASN cc_start: 0.9274 (t0) cc_final: 0.8431 (t0) REVERT: j 45 ASP cc_start: 0.8836 (m-30) cc_final: 0.8262 (m-30) REVERT: I 15 GLN cc_start: 0.8648 (mt0) cc_final: 0.7942 (mt0) REVERT: I 18 GLU cc_start: 0.8538 (pp20) cc_final: 0.8233 (pp20) REVERT: I 19 LEU cc_start: 0.9250 (mp) cc_final: 0.8850 (mp) REVERT: L 272 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8404 (p90) REVERT: H 93 ASN cc_start: 0.8359 (t0) cc_final: 0.7975 (t0) REVERT: H 206 GLN cc_start: 0.8995 (mt0) cc_final: 0.8728 (pt0) REVERT: g 3 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8685 (tmmm) REVERT: g 5 TYR cc_start: 0.8669 (p90) cc_final: 0.8285 (p90) REVERT: g 38 ASN cc_start: 0.9348 (t0) cc_final: 0.9094 (t0) REVERT: d 38 ASN cc_start: 0.9431 (t0) cc_final: 0.9184 (t0) outliers start: 43 outliers final: 27 residues processed: 534 average time/residue: 0.5258 time to fit residues: 325.9548 Evaluate side-chains 522 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 487 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain t residue 33 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain r residue 26 LEU 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 J residue 24 LEU 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 15 GLN Chi-restraints excluded: chain R residue 24 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 207 MET 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 Chi-restraints excluded: chain B residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 160 optimal weight: 0.0060 chunk 205 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 20 GLN t 20 GLN e 20 GLN b 42 ASN ** k 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN M 78 GLN g 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064719 restraints weight = 58187.888| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.19 r_work: 0.2801 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3627 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= 0.172 Angle : 1.182 38.398 32317 Z= 0.479 Chirality : 0.044 0.446 3242 Planarity : 0.004 0.053 3934 Dihedral : 21.750 179.989 3985 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.95 % Allowed : 22.24 % Favored : 75.81 % 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: 1.74 (0.18), residues: 2286 helix: 1.90 (0.13), residues: 1585 sheet: 2.60 (1.66), residues: 10 loop : -0.63 (0.24), residues: 691 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 0.017 0.001 PHE t 17 TRP 0.014 0.001 TRP k 43 HIS 0.006 0.001 HIS X 5 Details of bonding type rmsd covalent geometry : bond 0.00424 (23465) covalent geometry : angle 1.18187 (32317) hydrogen bonds : bond 0.04922 ( 1309) hydrogen bonds : angle 4.31863 ( 3705) Misc. bond : bond 0.00110 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8909.83 seconds wall clock time: 151 minutes 49.42 seconds (9109.42 seconds total)