Starting phenix.real_space_refine on Mon Oct 13 11:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.cif Found real_map, /net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6et5_3951/10_2025/6et5_3951.map" } resolution = 2.87 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 Mg 38 5.21 5 S 45 5.16 5 C 22073 2.51 5 N 4821 2.21 5 O 5012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31994 Number of models: 1 Model: "" Number of chains: 92 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2603 Classifications: {'peptide': 333} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2555 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 303} Chain: "H" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2018 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "2" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "F" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "K" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "P" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "S" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "V" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "e" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "h" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "k" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "n" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "q" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "t" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "w" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Q" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "T" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "W" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Z" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "c" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "f" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "i" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "o" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "r" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "u" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "x" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "4" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "7" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "O" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "R" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "U" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "X" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "a" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "d" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "g" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "j" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "m" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "p" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "s" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "v" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "5" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 256 Unusual residues: {' FE': 1, 'BCB': 2, 'BPB': 1, 'UQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Unusual residues: {'BCB': 2, 'BPB': 1, 'LDA': 1, 'MQ9': 1, 'NS5': 1, 'SO4': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'LDA': 1, 'SO4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'BCB': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.67, per 1000 atoms: 0.24 Number of scatterers: 31994 At special positions: 0 Unit cell: (145.22, 145.22, 147.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 45 16.00 Mg 38 11.99 O 5012 8.00 N 4821 7.00 C 22073 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6526 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 9 sheets defined 59.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.572A pdb=" N VAL C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 101 through 121 removed outlier: 4.216A pdb=" N VAL C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.060A pdb=" N CYS C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 223 through 241 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.643A pdb=" N PHE C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.864A pdb=" N ALA C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.630A pdb=" N ASN C 286 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 310 removed outlier: 4.161A pdb=" N CYS C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 18 through 23 removed outlier: 4.421A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP L 23 " --> pdb=" O GLY L 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 18 through 23' Processing helix chain 'L' and resid 31 through 55 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.691A pdb=" N VAL L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Proline residue: L 124 - end of helix Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.847A pdb=" N HIS L 144 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 164 removed outlier: 4.034A pdb=" N LEU L 154 " --> pdb=" O ILE L 150 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR L 164 " --> pdb=" O PHE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 220 removed outlier: 3.507A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 251 removed outlier: 4.012A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 247 " --> pdb=" O THR L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.820A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'M' and resid 2 through 6 removed outlier: 4.103A pdb=" N THR M 5 " --> pdb=" O ASP M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 51 through 77 removed outlier: 4.097A pdb=" N GLY M 55 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 88 Processing helix chain 'M' and resid 89 through 91 No H-bonds generated for 'chain 'M' and resid 89 through 91' Processing helix chain 'M' and resid 110 through 138 Processing helix chain 'M' and resid 142 through 160 removed outlier: 3.504A pdb=" N ALA M 151 " --> pdb=" O ASN M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 167 Processing helix chain 'M' and resid 168 through 172 removed outlier: 3.559A pdb=" N GLU M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 191 removed outlier: 3.643A pdb=" N ILE M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M 184 " --> pdb=" O HIS M 180 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR M 185 " --> pdb=" O ILE M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 196 Processing helix chain 'M' and resid 197 through 224 Processing helix chain 'M' and resid 225 through 228 Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'M' and resid 240 through 255 Processing helix chain 'M' and resid 259 through 285 removed outlier: 4.313A pdb=" N HIS M 264 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 265 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET M 275 " --> pdb=" O SER M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 299 Processing helix chain 'M' and resid 314 through 318 Processing helix chain 'H' and resid 12 through 31 removed outlier: 3.715A pdb=" N TYR H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 106 through 111 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.624A pdb=" N ALA H 219 " --> pdb=" O GLU H 216 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 221 " --> pdb=" O PHE H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 249 removed outlier: 3.742A pdb=" N TYR H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 254 Processing helix chain 'z' and resid 7 through 9 No H-bonds generated for 'chain 'z' and resid 7 through 9' Processing helix chain 'z' and resid 10 through 16 removed outlier: 4.040A pdb=" N ASP z 16 " --> pdb=" O TRP z 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 40 Processing helix chain '1' and resid 16 through 42 removed outlier: 3.552A pdb=" N THR 1 42 " --> pdb=" O TYR 1 38 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 35 Proline residue: 2 27 - end of helix removed outlier: 3.941A pdb=" N TYR 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.697A pdb=" N ILE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 16 " --> pdb=" O TRP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 40 Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.810A pdb=" N ASP K 16 " --> pdb=" O TRP K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 41 Processing helix chain 'P' and resid 7 through 9 No H-bonds generated for 'chain 'P' and resid 7 through 9' Processing helix chain 'P' and resid 10 through 16 removed outlier: 3.832A pdb=" N ASP P 16 " --> pdb=" O TRP P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 41 Processing helix chain 'S' and resid 7 through 9 No H-bonds generated for 'chain 'S' and resid 7 through 9' Processing helix chain 'S' and resid 10 through 15 Processing helix chain 'S' and resid 16 through 40 Processing helix chain 'V' and resid 7 through 9 No H-bonds generated for 'chain 'V' and resid 7 through 9' Processing helix chain 'V' and resid 10 through 16 removed outlier: 3.715A pdb=" N ASP V 16 " --> pdb=" O TRP V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 40 Processing helix chain 'Y' and resid 7 through 9 No H-bonds generated for 'chain 'Y' and resid 7 through 9' Processing helix chain 'Y' and resid 10 through 16 removed outlier: 3.880A pdb=" N ASP Y 16 " --> pdb=" O TRP Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 40 Processing helix chain 'b' and resid 7 through 9 No H-bonds generated for 'chain 'b' and resid 7 through 9' Processing helix chain 'b' and resid 10 through 16 removed outlier: 3.817A pdb=" N ASP b 16 " --> pdb=" O TRP b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 40 Processing helix chain 'e' and resid 7 through 9 No H-bonds generated for 'chain 'e' and resid 7 through 9' Processing helix chain 'e' and resid 10 through 16 removed outlier: 3.935A pdb=" N ASP e 16 " --> pdb=" O TRP e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 40 Processing helix chain 'h' and resid 7 through 9 No H-bonds generated for 'chain 'h' and resid 7 through 9' Processing helix chain 'h' and resid 10 through 16 removed outlier: 3.791A pdb=" N ASP h 16 " --> pdb=" O TRP h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 41 Processing helix chain 'k' and resid 7 through 9 No H-bonds generated for 'chain 'k' and resid 7 through 9' Processing helix chain 'k' and resid 10 through 16 removed outlier: 3.550A pdb=" N ASP k 16 " --> pdb=" O TRP k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 41 Processing helix chain 'n' and resid 7 through 9 No H-bonds generated for 'chain 'n' and resid 7 through 9' Processing helix chain 'n' and resid 10 through 16 removed outlier: 3.523A pdb=" N ASP n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 41 Processing helix chain 'q' and resid 7 through 9 No H-bonds generated for 'chain 'q' and resid 7 through 9' Processing helix chain 'q' and resid 10 through 16 removed outlier: 3.751A pdb=" N ASP q 16 " --> pdb=" O TRP q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 40 Processing helix chain 't' and resid 7 through 10 Processing helix chain 't' and resid 11 through 16 removed outlier: 3.600A pdb=" N ASP t 16 " --> pdb=" O TRP t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 16 through 40 Processing helix chain 'w' and resid 7 through 9 No H-bonds generated for 'chain 'w' and resid 7 through 9' Processing helix chain 'w' and resid 10 through 16 removed outlier: 3.825A pdb=" N ASP w 16 " --> pdb=" O TRP w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 16 through 41 Processing helix chain '3' and resid 7 through 9 No H-bonds generated for 'chain '3' and resid 7 through 9' Processing helix chain '3' and resid 10 through 16 removed outlier: 3.502A pdb=" N ILE 3 14 " --> pdb=" O LYS 3 10 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 3 16 " --> pdb=" O TRP 3 12 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 41 Processing helix chain '6' and resid 7 through 9 No H-bonds generated for 'chain '6' and resid 7 through 9' Processing helix chain '6' and resid 10 through 16 removed outlier: 3.599A pdb=" N ILE 6 14 " --> pdb=" O LYS 6 10 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP 6 16 " --> pdb=" O TRP 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 16 through 40 removed outlier: 3.846A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 44 Processing helix chain 'N' and resid 16 through 44 Processing helix chain 'Q' and resid 16 through 44 Processing helix chain 'T' and resid 16 through 44 removed outlier: 3.540A pdb=" N ALA T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 44 removed outlier: 3.572A pdb=" N LEU W 30 " --> pdb=" O THR W 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 44 Processing helix chain 'c' and resid 16 through 44 Processing helix chain 'f' and resid 16 through 44 Processing helix chain 'i' and resid 16 through 44 Processing helix chain 'l' and resid 16 through 44 Processing helix chain 'o' and resid 16 through 44 Processing helix chain 'r' and resid 16 through 42 Processing helix chain 'u' and resid 16 through 44 Processing helix chain 'x' and resid 16 through 44 removed outlier: 3.602A pdb=" N THR x 42 " --> pdb=" O TYR x 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA x 43 " --> pdb=" O LEU x 39 " (cutoff:3.500A) Processing helix chain '4' and resid 16 through 44 removed outlier: 3.546A pdb=" N ALA 4 43 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 44 removed outlier: 3.647A pdb=" N ALA 7 43 " --> pdb=" O LEU 7 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 35 Proline residue: I 27 - end of helix removed outlier: 3.960A pdb=" N TYR I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 35 Proline residue: O 27 - end of helix removed outlier: 3.856A pdb=" N TYR O 35 " --> pdb=" O ILE O 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 35 Proline residue: R 27 - end of helix removed outlier: 3.849A pdb=" N TYR R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 35 Proline residue: U 27 - end of helix removed outlier: 4.110A pdb=" N TYR U 35 " --> pdb=" O ILE U 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 35 Proline residue: X 27 - end of helix removed outlier: 4.004A pdb=" N TYR X 35 " --> pdb=" O ILE X 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 35 Proline residue: a 27 - end of helix removed outlier: 4.044A pdb=" N TYR a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 35 Proline residue: d 27 - end of helix removed outlier: 3.921A pdb=" N TYR d 35 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 35 Proline residue: g 27 - end of helix removed outlier: 4.023A pdb=" N TYR g 35 " --> pdb=" O ILE g 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 18 through 35 Proline residue: j 27 - end of helix removed outlier: 3.852A pdb=" N TYR j 35 " --> pdb=" O ILE j 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 18 through 35 Proline residue: m 27 - end of helix removed outlier: 3.830A pdb=" N TYR m 35 " --> pdb=" O ILE m 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 18 through 35 Proline residue: p 27 - end of helix removed outlier: 3.853A pdb=" N TYR p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 35 Proline residue: s 27 - end of helix removed outlier: 3.983A pdb=" N TYR s 35 " --> pdb=" O ILE s 31 " (cutoff:3.500A) Processing helix chain 'v' and resid 18 through 35 Proline residue: v 27 - end of helix removed outlier: 4.043A pdb=" N TYR v 35 " --> pdb=" O ILE v 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 35 Proline residue: y 27 - end of helix removed outlier: 3.978A pdb=" N TYR y 35 " --> pdb=" O ILE y 31 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 35 Proline residue: 5 27 - end of helix removed outlier: 3.777A pdb=" N TYR 5 35 " --> pdb=" O ILE 5 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'M' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 6.122A pdb=" N LEU H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.679A pdb=" N GLU H 184 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 171 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR H 182 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 173 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE H 180 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG H 192 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.641A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 4125 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: 5.45 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 9597 1.37 - 1.55: 22726 1.55 - 1.73: 703 1.73 - 1.90: 62 1.90 - 2.08: 164 Bond restraints: 33252 Sorted by residual: bond pdb=" CAB BCB q 101 " pdb=" CBB BCB q 101 " ideal model delta sigma weight residual 1.510 1.209 0.301 2.30e-02 1.89e+03 1.71e+02 bond pdb=" C2 UQ9 L 304 " pdb=" O2 UQ9 L 304 " ideal model delta sigma weight residual 1.213 1.426 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C2 UQ9 6 101 " pdb=" O2 UQ9 6 101 " ideal model delta sigma weight residual 1.213 1.423 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C28 UQ9 L 304 " pdb=" C29 UQ9 L 304 " ideal model delta sigma weight residual 1.335 1.534 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C48 UQ9 L 304 " pdb=" C49 UQ9 L 304 " ideal model delta sigma weight residual 1.336 1.534 -0.198 2.00e-02 2.50e+03 9.79e+01 ... (remaining 33247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 43171 5.31 - 10.63: 2287 10.63 - 15.94: 427 15.94 - 21.26: 126 21.26 - 26.57: 6 Bond angle restraints: 46017 Sorted by residual: angle pdb=" C TRP P 48 " pdb=" CA TRP P 48 " pdb=" CB TRP P 48 " ideal model delta sigma weight residual 111.82 97.11 14.71 1.28e+00 6.10e-01 1.32e+02 angle pdb=" C TRP e 48 " pdb=" CA TRP e 48 " pdb=" CB TRP e 48 " ideal model delta sigma weight residual 111.82 97.36 14.46 1.28e+00 6.10e-01 1.28e+02 angle pdb=" C TRP b 48 " pdb=" CA TRP b 48 " pdb=" CB TRP b 48 " ideal model delta sigma weight residual 111.73 96.55 15.18 1.42e+00 4.96e-01 1.14e+02 angle pdb=" N TYR L 164 " pdb=" CA TYR L 164 " pdb=" C TYR L 164 " ideal model delta sigma weight residual 110.17 93.58 16.59 1.61e+00 3.86e-01 1.06e+02 angle pdb=" N ILE G 47 " pdb=" CA ILE G 47 " pdb=" C ILE G 47 " ideal model delta sigma weight residual 110.42 119.83 -9.41 9.60e-01 1.09e+00 9.60e+01 ... (remaining 46012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16812 35.58 - 71.15: 955 71.15 - 106.73: 124 106.73 - 142.31: 25 142.31 - 177.88: 9 Dihedral angle restraints: 17925 sinusoidal: 7827 harmonic: 10098 Sorted by residual: dihedral pdb=" CBD BCB 6 102 " pdb=" CGD BCB 6 102 " pdb=" O2D BCB 6 102 " pdb=" CED BCB 6 102 " ideal model delta sinusoidal sigma weight residual -180.00 -59.22 -120.78 1 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C1 BCB u 101 " pdb=" CGA BCB u 101 " pdb=" O2A BCB u 101 " pdb=" CBA BCB u 101 " ideal model delta sinusoidal sigma weight residual -180.00 -2.12 -177.88 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCB i 101 " pdb=" CGA BCB i 101 " pdb=" O2A BCB i 101 " pdb=" CBA BCB i 101 " ideal model delta sinusoidal sigma weight residual 180.00 2.81 177.19 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 17922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 4798 1.045 - 2.089: 13 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 2 Chirality restraints: 4813 Sorted by residual: chirality pdb=" C13 BPB M 407 " pdb=" C12 BPB M 407 " pdb=" C14 BPB M 407 " pdb=" C15 BPB M 407 " both_signs ideal model delta sigma weight residual False 2.60 -2.63 5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C13 BPB L 303 " pdb=" C12 BPB L 303 " pdb=" C14 BPB L 303 " pdb=" C15 BPB L 303 " both_signs ideal model delta sigma weight residual False 2.60 -2.54 5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA LEU P 40 " pdb=" N LEU P 40 " pdb=" C LEU P 40 " pdb=" CB LEU P 40 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.34e+01 ... (remaining 4810 not shown) Planarity restraints: 5558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 6 101 " 0.144 2.00e-02 2.50e+03 2.58e-01 1.99e+03 pdb=" C1M UQ9 6 101 " 0.227 2.00e-02 2.50e+03 pdb=" C2 UQ9 6 101 " 0.254 2.00e-02 2.50e+03 pdb=" C3 UQ9 6 101 " 0.153 2.00e-02 2.50e+03 pdb=" C4 UQ9 6 101 " 0.043 2.00e-02 2.50e+03 pdb=" C5 UQ9 6 101 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 6 101 " 0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 6 101 " -0.040 2.00e-02 2.50e+03 pdb=" O2 UQ9 6 101 " -0.738 2.00e-02 2.50e+03 pdb=" O3 UQ9 6 101 " 0.230 2.00e-02 2.50e+03 pdb=" O4 UQ9 6 101 " -0.053 2.00e-02 2.50e+03 pdb=" O5 UQ9 6 101 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 L 304 " 0.152 2.00e-02 2.50e+03 2.56e-01 1.97e+03 pdb=" C1M UQ9 L 304 " 0.224 2.00e-02 2.50e+03 pdb=" C2 UQ9 L 304 " 0.253 2.00e-02 2.50e+03 pdb=" C3 UQ9 L 304 " 0.144 2.00e-02 2.50e+03 pdb=" C4 UQ9 L 304 " 0.020 2.00e-02 2.50e+03 pdb=" C5 UQ9 L 304 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 L 304 " 0.035 2.00e-02 2.50e+03 pdb=" C7 UQ9 L 304 " -0.059 2.00e-02 2.50e+03 pdb=" O2 UQ9 L 304 " -0.733 2.00e-02 2.50e+03 pdb=" O3 UQ9 L 304 " 0.229 2.00e-02 2.50e+03 pdb=" O4 UQ9 L 304 " -0.044 2.00e-02 2.50e+03 pdb=" O5 UQ9 L 304 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA NS0 i 102 " 0.295 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CB NS0 i 102 " -0.589 2.00e-02 2.50e+03 pdb=" CG NS0 i 102 " 0.293 2.00e-02 2.50e+03 pdb=" CD1 NS0 i 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 NS0 i 102 " -0.006 2.00e-02 2.50e+03 ... (remaining 5555 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 32 2.25 - 2.92: 13033 2.92 - 3.58: 46804 3.58 - 4.24: 80731 4.24 - 4.90: 130118 Nonbonded interactions: 270718 Sorted by model distance: nonbonded pdb=" CD1 ILE f 47 " pdb=" CD1 LEU d 17 " model vdw 1.592 3.880 nonbonded pdb=" CD1 ILE N 47 " pdb=" CD1 LEU I 17 " model vdw 1.701 3.880 nonbonded pdb=" O TRP L 25 " pdb=" NH2 ARG 3 19 " model vdw 1.791 3.120 nonbonded pdb=" CG1 ILE 1 21 " pdb=" C8 NS0 1 102 " model vdw 1.856 3.088 nonbonded pdb=" O ALA 6 23 " pdb=" CD2 TYR 6 27 " model vdw 1.863 3.340 ... (remaining 270713 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 '1' selection = chain '4' selection = chain '7' selection = chain 'G' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'I' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'y' } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain '6' and resid 1 through 58) selection = (chain 'F' and resid 1 through 58) selection = (chain 'K' and resid 1 through 58) selection = (chain 'P' and resid 1 through 58) selection = (chain 'S' and resid 1 through 58) selection = (chain 'V' and resid 1 through 58) selection = (chain 'Y' and resid 1 through 58) selection = (chain 'b' and resid 1 through 58) selection = (chain 'e' and resid 1 through 58) selection = (chain 'h' and resid 1 through 58) selection = (chain 'k' and resid 1 through 58) selection = (chain 'n' and resid 1 through 58) selection = (chain 'q' and resid 1 through 58) selection = (chain 't' and resid 1 through 58) selection = (chain 'w' and resid 1 through 58) selection = (chain 'z' and resid 1 through 58) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.510 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.028 0.767 33312 Z= 1.737 Angle : 2.859 26.570 46017 Z= 1.477 Chirality : 0.206 5.223 4813 Planarity : 0.029 0.350 5558 Dihedral : 21.889 177.884 11399 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 4.08 % Allowed : 12.22 % Favored : 83.70 % Rotamer: Outliers : 8.13 % Allowed : 12.88 % Favored : 79.00 % Cbeta Deviations : 6.19 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 1.02 % 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 aren not related in a simple way. whole: -5.05 (0.11), residues: 3380 helix: -2.60 (0.09), residues: 1693 sheet: -2.28 (0.87), residues: 26 loop : -4.33 (0.12), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 146 TYR 0.056 0.005 TYR C 227 PHE 0.045 0.005 PHE L 62 TRP 0.056 0.007 TRP L 86 HIS 0.019 0.004 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.02514 (33252) covalent geometry : angle 2.85920 (46017) hydrogen bonds : bond 0.21483 ( 1416) hydrogen bonds : angle 8.44019 ( 4125) Misc. bond : bond 0.27642 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 713 time to evaluate : 1.237 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: C 74 MET cc_start: 0.9558 (mmp) cc_final: 0.9288 (mmt) REVERT: C 110 MET cc_start: 0.9562 (mmt) cc_final: 0.9160 (mmt) REVERT: C 113 MET cc_start: 0.9602 (ttp) cc_final: 0.9345 (ttp) REVERT: C 123 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9253 (pm20) REVERT: C 233 MET cc_start: 0.9340 (mmp) cc_final: 0.8443 (mmt) REVERT: C 252 THR cc_start: 0.9671 (OUTLIER) cc_final: 0.9463 (p) REVERT: C 273 MET cc_start: 0.9485 (ttp) cc_final: 0.9284 (ttt) REVERT: L 23 ASP cc_start: 0.9598 (t0) cc_final: 0.9270 (t0) REVERT: L 106 GLU cc_start: 0.9754 (mt-10) cc_final: 0.9545 (mm-30) REVERT: L 204 ASP cc_start: 0.9350 (m-30) cc_final: 0.9107 (m-30) REVERT: L 228 SER cc_start: 0.9564 (OUTLIER) cc_final: 0.9272 (p) REVERT: H 133 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9324 (ttmp) REVERT: H 161 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8716 (p0) REVERT: H 217 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: H 237 LYS cc_start: 0.9674 (OUTLIER) cc_final: 0.9384 (mmtp) REVERT: H 239 SER cc_start: 0.9859 (m) cc_final: 0.9623 (p) REVERT: z 14 ILE cc_start: 0.9704 (mm) cc_final: 0.9336 (tp) REVERT: 2 34 THR cc_start: 0.9477 (m) cc_final: 0.9249 (p) REVERT: F 31 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9312 (pp) REVERT: F 44 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8728 (ttt-90) REVERT: K 18 ARG cc_start: 0.9333 (mtm110) cc_final: 0.8777 (tmt170) REVERT: b 44 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.8943 (mtm180) REVERT: h 43 ASP cc_start: 0.9780 (m-30) cc_final: 0.9480 (m-30) REVERT: h 51 GLN cc_start: 0.9537 (tp40) cc_final: 0.9330 (mm-40) REVERT: k 56 LYS cc_start: 0.9319 (tmtp) cc_final: 0.9008 (mppt) REVERT: w 52 ARG cc_start: 0.9348 (mtm-85) cc_final: 0.9078 (ppt170) REVERT: 3 16 ASP cc_start: 0.9333 (t0) cc_final: 0.8685 (t0) REVERT: 3 27 TYR cc_start: 0.9342 (t80) cc_final: 0.9117 (t80) REVERT: 6 4 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7338 (m-10) REVERT: c 44 ARG cc_start: 0.9497 (OUTLIER) cc_final: 0.9263 (mmp80) REVERT: l 29 TYR cc_start: 0.9512 (t80) cc_final: 0.9279 (t80) REVERT: o 16 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (ptpt) REVERT: r 16 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8804 (mttp) REVERT: d 16 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6364 (t0) REVERT: s 35 TYR cc_start: 0.9453 (m-80) cc_final: 0.8938 (m-10) outliers start: 238 outliers final: 55 residues processed: 873 average time/residue: 0.5591 time to fit residues: 595.1547 Evaluate side-chains 528 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 458 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain b residue 44 ARG Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 6 residue 4 TYR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain Z residue 14 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 44 ARG Chi-restraints excluded: chain f residue 13 GLU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain i residue 14 GLU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain l residue 14 GLU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 23 VAL Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 14 GLU Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain x residue 14 GLU Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 14 GLU Chi-restraints excluded: chain 7 residue 34 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 17 LEU Chi-restraints excluded: chain s residue 26 ILE Chi-restraints excluded: chain y residue 14 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN L 55 GLN L 144 HIS L 211 HIS L 239 ASN H 58 GLN H 106 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043911 restraints weight = 113120.882| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 4.22 r_work: 0.2515 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.688 33312 Z= 0.240 Angle : 1.163 18.813 46017 Z= 0.517 Chirality : 0.056 0.973 4813 Planarity : 0.006 0.074 5558 Dihedral : 20.640 179.887 5342 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.08 % Favored : 90.41 % Rotamer: Outliers : 5.57 % Allowed : 23.26 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 aren not related in a simple way. whole: -2.21 (0.14), residues: 3380 helix: 0.26 (0.11), residues: 1792 sheet: 0.02 (1.09), residues: 22 loop : -3.78 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 52 TYR 0.017 0.002 TYR 6 27 PHE 0.027 0.002 PHE 7 18 TRP 0.042 0.003 TRP O 15 HIS 0.011 0.001 HIS M 16 Details of bonding type rmsd covalent geometry : bond 0.00573 (33252) covalent geometry : angle 1.16320 (46017) hydrogen bonds : bond 0.07128 ( 1416) hydrogen bonds : angle 5.38561 ( 4125) Misc. bond : bond 0.11125 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 587 time to evaluate : 1.195 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: C 37 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: C 110 MET cc_start: 0.9723 (mmt) cc_final: 0.8683 (mmt) REVERT: C 113 MET cc_start: 0.9760 (ttp) cc_final: 0.9169 (ttp) REVERT: C 117 ILE cc_start: 0.9725 (mp) cc_final: 0.9521 (mp) REVERT: C 146 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8725 (mmm-85) REVERT: C 149 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: C 238 ASP cc_start: 0.9649 (t0) cc_final: 0.9323 (t0) REVERT: C 252 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9168 (p) REVERT: C 312 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9068 (m) REVERT: L 23 ASP cc_start: 0.9012 (t0) cc_final: 0.8514 (t0) REVERT: L 29 TYR cc_start: 0.9414 (m-80) cc_final: 0.8925 (m-80) REVERT: L 60 ASP cc_start: 0.8515 (t0) cc_final: 0.8121 (t0) REVERT: L 148 TYR cc_start: 0.9369 (m-80) cc_final: 0.9085 (m-80) REVERT: L 204 ASP cc_start: 0.8728 (m-30) cc_final: 0.8333 (m-30) REVERT: L 210 GLU cc_start: 0.8862 (mp0) cc_final: 0.8648 (mp0) REVERT: M 22 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8505 (tm-30) REVERT: M 26 ASN cc_start: 0.9609 (m-40) cc_final: 0.9135 (p0) REVERT: M 171 GLU cc_start: 0.9510 (OUTLIER) cc_final: 0.9058 (mp0) REVERT: M 193 ASN cc_start: 0.9387 (t0) cc_final: 0.8829 (t0) REVERT: H 66 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: H 89 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8747 (mtpm) REVERT: H 92 GLN cc_start: 0.8936 (pm20) cc_final: 0.8613 (pm20) REVERT: H 133 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8700 (tppp) REVERT: H 134 ILE cc_start: 0.9614 (mt) cc_final: 0.9353 (mm) REVERT: H 204 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7739 (mmmm) REVERT: H 239 SER cc_start: 0.9737 (m) cc_final: 0.9418 (p) REVERT: 2 34 THR cc_start: 0.9350 (m) cc_final: 0.8978 (p) REVERT: F 35 ILE cc_start: 0.9726 (OUTLIER) cc_final: 0.9492 (mp) REVERT: K 10 LYS cc_start: 0.9745 (OUTLIER) cc_final: 0.9459 (mmmm) REVERT: K 18 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8670 (tmt170) REVERT: P 43 ASP cc_start: 0.9061 (m-30) cc_final: 0.8579 (t0) REVERT: S 10 LYS cc_start: 0.9672 (OUTLIER) cc_final: 0.9249 (mmmm) REVERT: Y 16 ASP cc_start: 0.8938 (t0) cc_final: 0.8468 (t0) REVERT: e 51 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8499 (mm-40) REVERT: e 56 LYS cc_start: 0.8986 (tmmt) cc_final: 0.8738 (tptp) REVERT: k 20 VAL cc_start: 0.9685 (t) cc_final: 0.9465 (p) REVERT: n 11 LEU cc_start: 0.9774 (tp) cc_final: 0.9361 (pt) REVERT: q 10 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.9335 (mmmm) REVERT: q 14 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.7950 (tp) REVERT: q 20 VAL cc_start: 0.9721 (t) cc_final: 0.9515 (p) REVERT: q 25 PHE cc_start: 0.9072 (t80) cc_final: 0.8839 (t80) REVERT: w 19 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8201 (mpt180) REVERT: w 51 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8812 (mm-40) REVERT: 3 16 ASP cc_start: 0.8279 (t0) cc_final: 0.7872 (t0) REVERT: 3 49 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8658 (tp30) REVERT: 6 18 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8531 (mpt90) REVERT: 6 51 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8460 (tp-100) REVERT: 6 56 LYS cc_start: 0.8215 (tmmm) cc_final: 0.7822 (tptp) REVERT: G 36 VAL cc_start: 0.9695 (t) cc_final: 0.9348 (p) REVERT: N 16 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8435 (ptpp) REVERT: W 16 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8789 (ptpp) REVERT: Z 16 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8742 (pmtt) REVERT: i 30 LEU cc_start: 0.9794 (mt) cc_final: 0.9574 (mm) REVERT: i 50 ILE cc_start: 0.9670 (pp) cc_final: 0.9353 (mm) REVERT: o 36 VAL cc_start: 0.9794 (t) cc_final: 0.9569 (p) REVERT: r 16 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8613 (mttp) REVERT: r 50 ILE cc_start: 0.9615 (pp) cc_final: 0.9245 (mp) REVERT: O 24 LEU cc_start: 0.9667 (mm) cc_final: 0.9118 (mm) REVERT: d 24 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9047 (mm) REVERT: g 24 LEU cc_start: 0.9415 (mt) cc_final: 0.8905 (mt) REVERT: m 24 LEU cc_start: 0.9452 (mm) cc_final: 0.9231 (mm) REVERT: y 21 LEU cc_start: 0.9533 (mt) cc_final: 0.9319 (mm) outliers start: 163 outliers final: 36 residues processed: 691 average time/residue: 0.4895 time to fit residues: 425.7217 Evaluate side-chains 542 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 486 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain z residue 4 TYR Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 45 LEU Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain 6 residue 18 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 16 LYS Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 27 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain v residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 164 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN H 102 GLN S 46 ASN h 46 ASN q 46 ASN 3 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.045972 restraints weight = 112712.630| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 4.29 r_work: 0.2571 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.642 33312 Z= 0.182 Angle : 1.005 19.383 46017 Z= 0.434 Chirality : 0.048 0.563 4813 Planarity : 0.005 0.067 5558 Dihedral : 18.564 179.294 5245 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.85 % Favored : 90.77 % Rotamer: Outliers : 5.19 % Allowed : 24.49 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -1.17 (0.15), residues: 3380 helix: 1.20 (0.12), residues: 1790 sheet: 0.79 (1.13), residues: 22 loop : -3.42 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 52 TYR 0.021 0.001 TYR R 35 PHE 0.022 0.001 PHE 7 18 TRP 0.029 0.002 TRP m 30 HIS 0.011 0.001 HIS o 19 Details of bonding type rmsd covalent geometry : bond 0.00434 (33252) covalent geometry : angle 1.00530 (46017) hydrogen bonds : bond 0.05815 ( 1416) hydrogen bonds : angle 4.97913 ( 4125) Misc. bond : bond 0.09655 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 593 time to evaluate : 1.190 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: C 37 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8749 (mp10) REVERT: C 110 MET cc_start: 0.9704 (mmt) cc_final: 0.8935 (mmt) REVERT: C 113 MET cc_start: 0.9779 (ttp) cc_final: 0.9240 (ttp) REVERT: C 117 ILE cc_start: 0.9731 (OUTLIER) cc_final: 0.9500 (mp) REVERT: C 149 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: C 238 ASP cc_start: 0.9586 (t0) cc_final: 0.9259 (t0) REVERT: C 252 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8759 (p) REVERT: L 23 ASP cc_start: 0.8883 (t0) cc_final: 0.8501 (t0) REVERT: L 29 TYR cc_start: 0.9421 (m-80) cc_final: 0.8970 (m-80) REVERT: L 60 ASP cc_start: 0.8680 (t0) cc_final: 0.8321 (t0) REVERT: L 148 TYR cc_start: 0.9307 (m-80) cc_final: 0.9060 (m-10) REVERT: L 204 ASP cc_start: 0.8902 (m-30) cc_final: 0.8510 (m-30) REVERT: L 210 GLU cc_start: 0.9062 (mp0) cc_final: 0.8785 (mp0) REVERT: L 212 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: M 9 GLN cc_start: 0.8999 (mt0) cc_final: 0.8706 (mt0) REVERT: M 22 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8621 (tm-30) REVERT: M 26 ASN cc_start: 0.9658 (m-40) cc_final: 0.9270 (p0) REVERT: M 97 LYS cc_start: 0.9517 (mttt) cc_final: 0.9268 (mmmm) REVERT: M 171 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9165 (mp0) REVERT: M 193 ASN cc_start: 0.9422 (t0) cc_final: 0.8924 (t0) REVERT: H 66 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8283 (mtpt) REVERT: H 92 GLN cc_start: 0.9054 (pm20) cc_final: 0.8305 (pm20) REVERT: H 102 GLN cc_start: 0.8979 (mt0) cc_final: 0.8529 (pm20) REVERT: H 131 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8919 (mtpp) REVERT: H 133 LYS cc_start: 0.8810 (tptp) cc_final: 0.8596 (tptp) REVERT: H 134 ILE cc_start: 0.9595 (mt) cc_final: 0.9302 (mm) REVERT: H 239 SER cc_start: 0.9720 (m) cc_final: 0.9404 (p) REVERT: z 16 ASP cc_start: 0.9031 (t0) cc_final: 0.8818 (t0) REVERT: z 52 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8526 (mtm180) REVERT: z 56 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8414 (tptp) REVERT: 2 34 THR cc_start: 0.9438 (m) cc_final: 0.9222 (p) REVERT: F 35 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9437 (mp) REVERT: K 10 LYS cc_start: 0.9696 (OUTLIER) cc_final: 0.9383 (mmmm) REVERT: K 18 ARG cc_start: 0.9117 (mtm110) cc_final: 0.8670 (tmt170) REVERT: P 16 ASP cc_start: 0.8994 (t0) cc_final: 0.8367 (t0) REVERT: P 19 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7913 (tpp-160) REVERT: P 43 ASP cc_start: 0.9104 (m-30) cc_final: 0.8460 (t0) REVERT: S 10 LYS cc_start: 0.9659 (OUTLIER) cc_final: 0.9273 (mmmm) REVERT: S 16 ASP cc_start: 0.8759 (t0) cc_final: 0.8244 (t0) REVERT: V 52 ARG cc_start: 0.9317 (ttp80) cc_final: 0.9116 (ttp-110) REVERT: Y 16 ASP cc_start: 0.8685 (t0) cc_final: 0.8183 (t0) REVERT: e 10 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.8959 (mmtp) REVERT: e 16 ASP cc_start: 0.8571 (t0) cc_final: 0.7822 (t0) REVERT: e 51 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8928 (mm-40) REVERT: e 56 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8801 (tptp) REVERT: h 16 ASP cc_start: 0.8483 (t0) cc_final: 0.7906 (t0) REVERT: h 27 TYR cc_start: 0.9379 (t80) cc_final: 0.9168 (t80) REVERT: h 52 ARG cc_start: 0.9130 (mtp-110) cc_final: 0.8862 (mtp-110) REVERT: k 20 VAL cc_start: 0.9632 (t) cc_final: 0.9425 (p) REVERT: k 56 LYS cc_start: 0.8810 (tppt) cc_final: 0.8274 (mppt) REVERT: n 3 GLU cc_start: 0.7571 (pp20) cc_final: 0.7316 (pm20) REVERT: n 11 LEU cc_start: 0.9754 (tp) cc_final: 0.9366 (pt) REVERT: n 16 ASP cc_start: 0.8539 (t0) cc_final: 0.8065 (t0) REVERT: q 10 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9264 (mmmm) REVERT: q 25 PHE cc_start: 0.9079 (t80) cc_final: 0.8797 (t80) REVERT: t 16 ASP cc_start: 0.8747 (t0) cc_final: 0.8278 (t0) REVERT: w 30 VAL cc_start: 0.9664 (t) cc_final: 0.9450 (p) REVERT: 3 16 ASP cc_start: 0.8080 (t0) cc_final: 0.7760 (t0) REVERT: 3 43 ASP cc_start: 0.9470 (m-30) cc_final: 0.9097 (m-30) REVERT: 3 49 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8707 (tp30) REVERT: 6 51 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8823 (tp-100) REVERT: 6 56 LYS cc_start: 0.8473 (tmmm) cc_final: 0.8097 (tptp) REVERT: G 28 LEU cc_start: 0.9494 (mt) cc_final: 0.9294 (mt) REVERT: G 36 VAL cc_start: 0.9659 (t) cc_final: 0.9331 (p) REVERT: Q 16 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8148 (ptpt) REVERT: T 36 VAL cc_start: 0.9607 (t) cc_final: 0.9208 (p) REVERT: W 16 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8860 (ptpp) REVERT: c 16 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8865 (ptpp) REVERT: i 30 LEU cc_start: 0.9773 (mt) cc_final: 0.9489 (mm) REVERT: o 36 VAL cc_start: 0.9722 (t) cc_final: 0.9466 (p) REVERT: r 16 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8457 (mttp) REVERT: u 36 VAL cc_start: 0.9582 (t) cc_final: 0.9206 (p) REVERT: O 24 LEU cc_start: 0.9495 (mm) cc_final: 0.9209 (mm) REVERT: d 24 LEU cc_start: 0.9322 (mm) cc_final: 0.9012 (mm) REVERT: d 26 ILE cc_start: 0.9506 (mm) cc_final: 0.9296 (mp) REVERT: y 21 LEU cc_start: 0.9500 (mt) cc_final: 0.9277 (mm) REVERT: 5 16 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7196 (t0) outliers start: 152 outliers final: 41 residues processed: 686 average time/residue: 0.4553 time to fit residues: 397.6976 Evaluate side-chains 564 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 504 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain z residue 56 LYS Chi-restraints excluded: chain 1 residue 16 LYS Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain 3 residue 51 GLN Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain 5 residue 16 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 244 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 307 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 214 GLN S 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.044955 restraints weight = 113732.132| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.31 r_work: 0.2557 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.771 33312 Z= 0.207 Angle : 0.963 17.851 46017 Z= 0.411 Chirality : 0.047 0.333 4813 Planarity : 0.005 0.075 5558 Dihedral : 17.581 179.503 5224 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.32 % Favored : 90.24 % Rotamer: Outliers : 5.09 % Allowed : 25.55 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.92 (0.15), residues: 3380 helix: 1.41 (0.12), residues: 1789 sheet: 0.23 (1.02), residues: 32 loop : -3.30 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 52 TYR 0.024 0.001 TYR u 29 PHE 0.024 0.001 PHE 7 22 TRP 0.028 0.002 TRP m 30 HIS 0.006 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00504 (33252) covalent geometry : angle 0.96331 (46017) hydrogen bonds : bond 0.05509 ( 1416) hydrogen bonds : angle 4.94834 ( 4125) Misc. bond : bond 0.11745 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 543 time to evaluate : 1.206 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: C 37 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8737 (mp10) REVERT: C 110 MET cc_start: 0.9718 (mmt) cc_final: 0.8725 (mmt) REVERT: C 113 MET cc_start: 0.9796 (ttp) cc_final: 0.9286 (ttp) REVERT: C 146 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8800 (mmm-85) REVERT: C 149 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: C 238 ASP cc_start: 0.9545 (t0) cc_final: 0.9223 (t0) REVERT: C 252 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8808 (p) REVERT: L 23 ASP cc_start: 0.8852 (t0) cc_final: 0.8543 (t0) REVERT: L 29 TYR cc_start: 0.9477 (m-80) cc_final: 0.9227 (m-80) REVERT: L 60 ASP cc_start: 0.8842 (t0) cc_final: 0.8395 (t0) REVERT: L 106 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8963 (mm-30) REVERT: L 148 TYR cc_start: 0.9312 (m-80) cc_final: 0.9040 (m-80) REVERT: L 204 ASP cc_start: 0.8987 (m-30) cc_final: 0.8606 (m-30) REVERT: L 210 GLU cc_start: 0.9134 (mp0) cc_final: 0.8864 (mp0) REVERT: L 212 GLU cc_start: 0.9477 (OUTLIER) cc_final: 0.8979 (pm20) REVERT: L 214 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8947 (tp40) REVERT: M 9 GLN cc_start: 0.9149 (mt0) cc_final: 0.8608 (mt0) REVERT: M 22 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8618 (tm-30) REVERT: M 26 ASN cc_start: 0.9660 (m-40) cc_final: 0.9321 (p0) REVERT: M 97 LYS cc_start: 0.9508 (mttt) cc_final: 0.9230 (mmmm) REVERT: M 171 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9101 (mp0) REVERT: M 193 ASN cc_start: 0.9468 (t0) cc_final: 0.9000 (t0) REVERT: M 261 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8995 (tm-30) REVERT: H 66 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8342 (mtpt) REVERT: H 92 GLN cc_start: 0.9217 (pm20) cc_final: 0.8598 (pm20) REVERT: H 102 GLN cc_start: 0.8899 (mt0) cc_final: 0.8539 (pm20) REVERT: H 131 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8930 (mtpp) REVERT: H 239 SER cc_start: 0.9737 (m) cc_final: 0.9411 (p) REVERT: F 54 LEU cc_start: 0.9041 (mp) cc_final: 0.8831 (pp) REVERT: K 10 LYS cc_start: 0.9698 (OUTLIER) cc_final: 0.9430 (mmmm) REVERT: K 16 ASP cc_start: 0.8464 (t0) cc_final: 0.7535 (t0) REVERT: K 18 ARG cc_start: 0.9153 (mtm110) cc_final: 0.8706 (tmt170) REVERT: K 43 ASP cc_start: 0.9301 (m-30) cc_final: 0.9081 (m-30) REVERT: P 16 ASP cc_start: 0.8865 (t0) cc_final: 0.8130 (t0) REVERT: P 19 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7756 (tpp-160) REVERT: P 43 ASP cc_start: 0.9182 (m-30) cc_final: 0.8507 (t0) REVERT: S 10 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.9262 (mmmm) REVERT: S 16 ASP cc_start: 0.8799 (t0) cc_final: 0.8270 (t0) REVERT: S 19 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7589 (tpp-160) REVERT: V 43 ASP cc_start: 0.9361 (m-30) cc_final: 0.9082 (m-30) REVERT: V 52 ARG cc_start: 0.9303 (ttp80) cc_final: 0.9064 (ttp80) REVERT: Y 15 LEU cc_start: 0.9513 (tp) cc_final: 0.9080 (tm) REVERT: Y 19 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7498 (mmp80) REVERT: Y 51 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8730 (tp-100) REVERT: e 10 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9001 (mmtp) REVERT: e 16 ASP cc_start: 0.8488 (t0) cc_final: 0.7817 (t0) REVERT: e 51 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8820 (mm-40) REVERT: h 16 ASP cc_start: 0.8404 (t0) cc_final: 0.7784 (OUTLIER) REVERT: h 52 ARG cc_start: 0.9156 (mtp-110) cc_final: 0.8870 (mtm-85) REVERT: n 11 LEU cc_start: 0.9770 (tp) cc_final: 0.9385 (pt) REVERT: n 16 ASP cc_start: 0.8438 (t0) cc_final: 0.7966 (t0) REVERT: n 56 LYS cc_start: 0.8883 (tppt) cc_final: 0.8672 (tppt) REVERT: q 10 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9314 (mmmm) REVERT: q 15 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8783 (mm) REVERT: q 16 ASP cc_start: 0.8246 (t0) cc_final: 0.7571 (t0) REVERT: q 25 PHE cc_start: 0.9082 (t80) cc_final: 0.8784 (t80) REVERT: t 16 ASP cc_start: 0.8659 (t0) cc_final: 0.8131 (t0) REVERT: t 54 LEU cc_start: 0.9044 (mm) cc_final: 0.8815 (mt) REVERT: 3 16 ASP cc_start: 0.8113 (t0) cc_final: 0.7745 (t0) REVERT: 3 43 ASP cc_start: 0.9497 (m-30) cc_final: 0.9047 (m-30) REVERT: 6 16 ASP cc_start: 0.8211 (t0) cc_final: 0.7471 (t0) REVERT: 6 51 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8909 (tp-100) REVERT: 6 56 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8326 (tppt) REVERT: G 36 VAL cc_start: 0.9625 (t) cc_final: 0.9329 (p) REVERT: T 36 VAL cc_start: 0.9603 (t) cc_final: 0.9236 (p) REVERT: Z 17 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: i 30 LEU cc_start: 0.9788 (mt) cc_final: 0.9565 (mm) REVERT: o 36 VAL cc_start: 0.9736 (t) cc_final: 0.9472 (p) REVERT: u 36 VAL cc_start: 0.9572 (t) cc_final: 0.9214 (p) REVERT: 4 16 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8915 (ptpp) REVERT: O 24 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9261 (mm) REVERT: d 26 ILE cc_start: 0.9502 (mm) cc_final: 0.9286 (mp) REVERT: d 35 TYR cc_start: 0.9459 (m-10) cc_final: 0.9209 (m-10) REVERT: p 34 THR cc_start: 0.9557 (m) cc_final: 0.9272 (p) REVERT: s 34 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9327 (p) REVERT: v 34 THR cc_start: 0.9708 (OUTLIER) cc_final: 0.9367 (p) outliers start: 149 outliers final: 52 residues processed: 634 average time/residue: 0.4780 time to fit residues: 384.7594 Evaluate side-chains 569 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 496 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 19 ARG Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain 6 residue 56 LYS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 16 LYS Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain v residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 225 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 244 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 204 optimal weight: 0.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN S 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.045858 restraints weight = 113034.068| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.29 r_work: 0.2606 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.653 33312 Z= 0.155 Angle : 0.924 17.427 46017 Z= 0.391 Chirality : 0.045 0.318 4813 Planarity : 0.005 0.069 5558 Dihedral : 17.083 179.521 5217 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.31 % Favored : 91.24 % Rotamer: Outliers : 4.03 % Allowed : 26.91 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.77 (0.15), residues: 3380 helix: 1.44 (0.12), residues: 1798 sheet: 0.28 (1.04), residues: 32 loop : -3.13 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 52 TYR 0.025 0.001 TYR V 27 PHE 0.017 0.001 PHE L 235 TRP 0.026 0.002 TRP m 30 HIS 0.004 0.001 HIS M 16 Details of bonding type rmsd covalent geometry : bond 0.00371 (33252) covalent geometry : angle 0.92404 (46017) hydrogen bonds : bond 0.05082 ( 1416) hydrogen bonds : angle 4.87443 ( 4125) Misc. bond : bond 0.09291 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 564 time to evaluate : 1.165 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: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8766 (mp10) REVERT: C 110 MET cc_start: 0.9693 (mmt) cc_final: 0.8731 (mmt) REVERT: C 113 MET cc_start: 0.9784 (ttp) cc_final: 0.9284 (ttp) REVERT: C 149 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: C 238 ASP cc_start: 0.9528 (t0) cc_final: 0.9203 (t0) REVERT: C 252 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8665 (p) REVERT: L 23 ASP cc_start: 0.8806 (t0) cc_final: 0.8551 (t0) REVERT: L 29 TYR cc_start: 0.9446 (m-80) cc_final: 0.9242 (m-80) REVERT: L 60 ASP cc_start: 0.8831 (t0) cc_final: 0.8355 (t0) REVERT: L 106 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8931 (mm-30) REVERT: L 148 TYR cc_start: 0.9270 (m-80) cc_final: 0.8984 (m-80) REVERT: L 204 ASP cc_start: 0.8980 (m-30) cc_final: 0.8585 (m-30) REVERT: L 210 GLU cc_start: 0.9096 (mp0) cc_final: 0.8855 (mp0) REVERT: L 212 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: M 9 GLN cc_start: 0.9077 (mt0) cc_final: 0.8678 (mt0) REVERT: M 22 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8579 (tm-30) REVERT: M 26 ASN cc_start: 0.9644 (m-40) cc_final: 0.9323 (p0) REVERT: M 171 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9149 (mp0) REVERT: M 193 ASN cc_start: 0.9447 (t0) cc_final: 0.8965 (t0) REVERT: M 261 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8952 (tm-30) REVERT: H 66 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8230 (mtpt) REVERT: H 92 GLN cc_start: 0.9221 (pm20) cc_final: 0.8581 (pm20) REVERT: H 102 GLN cc_start: 0.8874 (mt0) cc_final: 0.8542 (pm20) REVERT: H 131 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8982 (mtpp) REVERT: H 134 ILE cc_start: 0.9601 (mt) cc_final: 0.9290 (mm) REVERT: H 217 GLN cc_start: 0.9517 (mt0) cc_final: 0.8997 (mp10) REVERT: H 239 SER cc_start: 0.9721 (m) cc_final: 0.9385 (p) REVERT: 2 34 THR cc_start: 0.9729 (OUTLIER) cc_final: 0.9337 (p) REVERT: F 54 LEU cc_start: 0.9020 (mp) cc_final: 0.8812 (pp) REVERT: K 10 LYS cc_start: 0.9684 (OUTLIER) cc_final: 0.9445 (mmmm) REVERT: K 16 ASP cc_start: 0.8442 (t0) cc_final: 0.7538 (t0) REVERT: K 18 ARG cc_start: 0.9193 (mtm110) cc_final: 0.8716 (tmt170) REVERT: K 43 ASP cc_start: 0.9262 (m-30) cc_final: 0.8860 (m-30) REVERT: P 16 ASP cc_start: 0.8768 (t0) cc_final: 0.7957 (t0) REVERT: P 52 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8723 (ptt180) REVERT: S 10 LYS cc_start: 0.9631 (OUTLIER) cc_final: 0.9307 (mmtp) REVERT: S 16 ASP cc_start: 0.8730 (t0) cc_final: 0.8185 (t0) REVERT: S 19 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7553 (tpp-160) REVERT: V 43 ASP cc_start: 0.9345 (m-30) cc_final: 0.8738 (m-30) REVERT: V 52 ARG cc_start: 0.9285 (ttp80) cc_final: 0.8712 (ttp80) REVERT: Y 14 ILE cc_start: 0.9396 (mp) cc_final: 0.9124 (tp) REVERT: e 10 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.8977 (mmtp) REVERT: e 47 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8683 (p90) REVERT: h 16 ASP cc_start: 0.8393 (t0) cc_final: 0.7801 (OUTLIER) REVERT: h 52 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8876 (mtm-85) REVERT: n 3 GLU cc_start: 0.7340 (pp20) cc_final: 0.7116 (pm20) REVERT: n 11 LEU cc_start: 0.9751 (tp) cc_final: 0.9384 (pt) REVERT: n 16 ASP cc_start: 0.8428 (t0) cc_final: 0.7922 (t0) REVERT: n 56 LYS cc_start: 0.8960 (tppt) cc_final: 0.8759 (tppt) REVERT: q 10 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9340 (mmmm) REVERT: q 16 ASP cc_start: 0.8299 (t0) cc_final: 0.7671 (t0) REVERT: q 25 PHE cc_start: 0.9027 (t80) cc_final: 0.8784 (t80) REVERT: t 15 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8907 (tp) REVERT: t 16 ASP cc_start: 0.8578 (t0) cc_final: 0.8040 (t0) REVERT: t 54 LEU cc_start: 0.9005 (mm) cc_final: 0.8783 (mt) REVERT: w 30 VAL cc_start: 0.9684 (t) cc_final: 0.9466 (p) REVERT: 3 16 ASP cc_start: 0.8069 (t0) cc_final: 0.7627 (t0) REVERT: 3 43 ASP cc_start: 0.9420 (m-30) cc_final: 0.9056 (m-30) REVERT: 3 49 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8576 (tp30) REVERT: 6 16 ASP cc_start: 0.8029 (t0) cc_final: 0.7229 (t0) REVERT: 6 51 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8838 (tp-100) REVERT: 6 56 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (tppt) REVERT: G 36 VAL cc_start: 0.9622 (t) cc_final: 0.9271 (p) REVERT: T 36 VAL cc_start: 0.9557 (t) cc_final: 0.9160 (p) REVERT: Z 17 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: i 30 LEU cc_start: 0.9777 (mt) cc_final: 0.9533 (mm) REVERT: o 36 VAL cc_start: 0.9705 (t) cc_final: 0.9431 (p) REVERT: r 16 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8814 (mttp) REVERT: u 36 VAL cc_start: 0.9537 (t) cc_final: 0.9162 (p) REVERT: 4 16 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8543 (ptpt) REVERT: 7 47 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9095 (pp) REVERT: I 31 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9307 (mt) REVERT: O 24 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9278 (mm) REVERT: g 31 ILE cc_start: 0.9508 (mt) cc_final: 0.9267 (mp) REVERT: s 34 THR cc_start: 0.9603 (t) cc_final: 0.9392 (p) REVERT: v 34 THR cc_start: 0.9753 (t) cc_final: 0.9447 (p) REVERT: 5 16 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7481 (t0) REVERT: 5 31 ILE cc_start: 0.9144 (mt) cc_final: 0.8923 (mt) outliers start: 118 outliers final: 42 residues processed: 633 average time/residue: 0.4587 time to fit residues: 371.5419 Evaluate side-chains 565 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 502 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain z residue 14 ILE Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 34 THR Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 6 residue 56 LYS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 16 LYS Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain 5 residue 16 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 219 optimal weight: 0.8980 chunk 134 optimal weight: 0.0570 chunk 133 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 overall best weight: 2.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.046689 restraints weight = 113121.464| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.21 r_work: 0.2608 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.638 33312 Z= 0.161 Angle : 0.912 14.566 46017 Z= 0.385 Chirality : 0.045 0.257 4813 Planarity : 0.005 0.094 5558 Dihedral : 16.664 179.658 5217 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.64 % Favored : 90.95 % Rotamer: Outliers : 3.86 % Allowed : 27.12 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.62 (0.15), residues: 3380 helix: 1.53 (0.12), residues: 1792 sheet: 0.26 (1.02), residues: 32 loop : -2.99 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG S 52 TYR 0.036 0.001 TYR d 35 PHE 0.031 0.001 PHE 7 22 TRP 0.025 0.002 TRP d 30 HIS 0.004 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00390 (33252) covalent geometry : angle 0.91156 (46017) hydrogen bonds : bond 0.04887 ( 1416) hydrogen bonds : angle 4.87124 ( 4125) Misc. bond : bond 0.09037 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 561 time to evaluate : 1.219 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: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: C 110 MET cc_start: 0.9676 (mmt) cc_final: 0.8856 (mmt) REVERT: C 146 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8789 (mmm-85) REVERT: C 149 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: C 188 ASP cc_start: 0.9253 (t0) cc_final: 0.8886 (t70) REVERT: C 238 ASP cc_start: 0.9502 (t0) cc_final: 0.9164 (t0) REVERT: C 252 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8872 (t) REVERT: L 23 ASP cc_start: 0.8831 (t0) cc_final: 0.8590 (t0) REVERT: L 29 TYR cc_start: 0.9485 (m-80) cc_final: 0.9263 (m-80) REVERT: L 60 ASP cc_start: 0.8846 (t0) cc_final: 0.8362 (t0) REVERT: L 148 TYR cc_start: 0.9278 (m-80) cc_final: 0.9046 (m-10) REVERT: L 204 ASP cc_start: 0.8990 (m-30) cc_final: 0.8619 (m-30) REVERT: L 210 GLU cc_start: 0.9138 (mp0) cc_final: 0.8918 (mp0) REVERT: L 212 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: M 9 GLN cc_start: 0.9075 (mt0) cc_final: 0.8684 (mt0) REVERT: M 22 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8564 (tm-30) REVERT: M 26 ASN cc_start: 0.9637 (m-40) cc_final: 0.9309 (p0) REVERT: M 171 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9039 (mp0) REVERT: M 193 ASN cc_start: 0.9430 (t0) cc_final: 0.8977 (t0) REVERT: H 66 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8343 (mtpp) REVERT: H 92 GLN cc_start: 0.9249 (pm20) cc_final: 0.8747 (pm20) REVERT: H 102 GLN cc_start: 0.8817 (mt0) cc_final: 0.8497 (pm20) REVERT: H 134 ILE cc_start: 0.9569 (mt) cc_final: 0.9266 (mm) REVERT: H 217 GLN cc_start: 0.9530 (mt0) cc_final: 0.8957 (mp10) REVERT: H 220 ASN cc_start: 0.9542 (m110) cc_final: 0.9166 (m-40) REVERT: K 10 LYS cc_start: 0.9692 (OUTLIER) cc_final: 0.9476 (mmmm) REVERT: K 16 ASP cc_start: 0.8395 (t0) cc_final: 0.7226 (t0) REVERT: K 18 ARG cc_start: 0.9188 (mtm110) cc_final: 0.8691 (tmt170) REVERT: K 29 THR cc_start: 0.9643 (m) cc_final: 0.9426 (m) REVERT: K 43 ASP cc_start: 0.9221 (m-30) cc_final: 0.8577 (t0) REVERT: P 16 ASP cc_start: 0.8668 (t0) cc_final: 0.7888 (t0) REVERT: P 52 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8688 (ptt180) REVERT: S 10 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9388 (mmtp) REVERT: S 16 ASP cc_start: 0.8737 (t0) cc_final: 0.8242 (t0) REVERT: S 19 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7518 (tpp-160) REVERT: S 52 ARG cc_start: 0.8992 (mtm110) cc_final: 0.8788 (mtm-85) REVERT: V 43 ASP cc_start: 0.9323 (m-30) cc_final: 0.8803 (m-30) REVERT: V 52 ARG cc_start: 0.9285 (ttp80) cc_final: 0.8703 (ttp80) REVERT: e 10 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9040 (mmtp) REVERT: h 16 ASP cc_start: 0.8300 (t0) cc_final: 0.7789 (t0) REVERT: h 52 ARG cc_start: 0.9200 (mtp-110) cc_final: 0.8923 (mtm-85) REVERT: n 11 LEU cc_start: 0.9758 (tp) cc_final: 0.9314 (pt) REVERT: n 16 ASP cc_start: 0.8432 (t0) cc_final: 0.7897 (t0) REVERT: n 56 LYS cc_start: 0.9008 (tppt) cc_final: 0.8761 (tppt) REVERT: q 10 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9151 (mmtp) REVERT: q 16 ASP cc_start: 0.8316 (t0) cc_final: 0.7783 (t0) REVERT: t 16 ASP cc_start: 0.8497 (t0) cc_final: 0.7831 (t0) REVERT: 3 16 ASP cc_start: 0.7928 (t0) cc_final: 0.7580 (t0) REVERT: 3 43 ASP cc_start: 0.9359 (m-30) cc_final: 0.9042 (m-30) REVERT: 3 44 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8288 (mtp-110) REVERT: 6 16 ASP cc_start: 0.7904 (t0) cc_final: 0.7096 (t0) REVERT: 6 51 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9013 (tp-100) REVERT: 6 56 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8501 (tptp) REVERT: G 36 VAL cc_start: 0.9590 (t) cc_final: 0.9325 (p) REVERT: Z 13 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: Z 17 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8796 (pm20) REVERT: i 30 LEU cc_start: 0.9781 (mt) cc_final: 0.9559 (mm) REVERT: o 36 VAL cc_start: 0.9726 (t) cc_final: 0.9444 (p) REVERT: u 36 VAL cc_start: 0.9522 (t) cc_final: 0.9190 (p) REVERT: x 16 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8350 (pmmt) REVERT: 4 16 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8960 (ptpp) REVERT: 7 47 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9053 (pp) REVERT: d 34 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9257 (p) REVERT: p 34 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9380 (p) REVERT: v 34 THR cc_start: 0.9728 (t) cc_final: 0.9510 (p) REVERT: 5 16 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7553 (t0) outliers start: 113 outliers final: 46 residues processed: 627 average time/residue: 0.4411 time to fit residues: 354.8848 Evaluate side-chains 578 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 510 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 14 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain 6 residue 56 LYS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 16 LYS Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain p residue 34 THR Chi-restraints excluded: chain 5 residue 16 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.0870 chunk 272 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN z 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.046648 restraints weight = 112940.021| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.25 r_work: 0.2629 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.592 33312 Z= 0.151 Angle : 0.911 18.699 46017 Z= 0.383 Chirality : 0.044 0.227 4813 Planarity : 0.005 0.075 5558 Dihedral : 16.475 179.391 5216 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.37 % Favored : 91.30 % Rotamer: Outliers : 3.35 % Allowed : 28.65 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.54 (0.15), residues: 3380 helix: 1.61 (0.12), residues: 1775 sheet: 0.23 (1.01), residues: 32 loop : -2.93 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG b 52 TYR 0.027 0.001 TYR V 27 PHE 0.025 0.001 PHE n 25 TRP 0.035 0.002 TRP m 30 HIS 0.003 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00370 (33252) covalent geometry : angle 0.91148 (46017) hydrogen bonds : bond 0.04681 ( 1416) hydrogen bonds : angle 4.85434 ( 4125) Misc. bond : bond 0.08466 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 551 time to evaluate : 1.228 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: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8766 (mp10) REVERT: C 110 MET cc_start: 0.9778 (mmt) cc_final: 0.8695 (mmt) REVERT: C 146 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8800 (mmm-85) REVERT: C 149 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: C 188 ASP cc_start: 0.9251 (t0) cc_final: 0.8815 (t0) REVERT: C 238 ASP cc_start: 0.9499 (t0) cc_final: 0.9159 (t0) REVERT: C 252 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8638 (p) REVERT: L 23 ASP cc_start: 0.8834 (t0) cc_final: 0.8584 (t0) REVERT: L 29 TYR cc_start: 0.9471 (m-80) cc_final: 0.9198 (m-80) REVERT: L 60 ASP cc_start: 0.8844 (t0) cc_final: 0.8336 (t0) REVERT: L 106 GLU cc_start: 0.9352 (tt0) cc_final: 0.8969 (mm-30) REVERT: L 127 MET cc_start: 0.9612 (tpp) cc_final: 0.9401 (tpp) REVERT: L 148 TYR cc_start: 0.9266 (m-80) cc_final: 0.9010 (m-80) REVERT: L 204 ASP cc_start: 0.8967 (m-30) cc_final: 0.8589 (m-30) REVERT: L 210 GLU cc_start: 0.9148 (mp0) cc_final: 0.8939 (mp0) REVERT: L 212 GLU cc_start: 0.9484 (OUTLIER) cc_final: 0.9147 (pm20) REVERT: M 9 GLN cc_start: 0.9081 (mt0) cc_final: 0.8685 (mt0) REVERT: M 22 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8566 (tm-30) REVERT: M 26 ASN cc_start: 0.9631 (m-40) cc_final: 0.9339 (p0) REVERT: M 171 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9021 (mp0) REVERT: M 193 ASN cc_start: 0.9445 (t0) cc_final: 0.9025 (t0) REVERT: H 66 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8370 (mtpp) REVERT: H 92 GLN cc_start: 0.9274 (pm20) cc_final: 0.8753 (pm20) REVERT: H 102 GLN cc_start: 0.8789 (mt0) cc_final: 0.8480 (pm20) REVERT: H 134 ILE cc_start: 0.9542 (mt) cc_final: 0.9245 (mm) REVERT: H 217 GLN cc_start: 0.9566 (mt0) cc_final: 0.9206 (mt0) REVERT: H 220 ASN cc_start: 0.9532 (m110) cc_final: 0.9146 (m-40) REVERT: K 16 ASP cc_start: 0.8418 (t0) cc_final: 0.7295 (t0) REVERT: K 18 ARG cc_start: 0.9204 (mtm110) cc_final: 0.8729 (tmt170) REVERT: K 29 THR cc_start: 0.9664 (m) cc_final: 0.9451 (m) REVERT: K 43 ASP cc_start: 0.9161 (m-30) cc_final: 0.8793 (m-30) REVERT: P 16 ASP cc_start: 0.8609 (t0) cc_final: 0.7817 (t0) REVERT: P 52 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8686 (ptt180) REVERT: S 10 LYS cc_start: 0.9638 (OUTLIER) cc_final: 0.9395 (mmtp) REVERT: S 16 ASP cc_start: 0.8607 (t0) cc_final: 0.8092 (t0) REVERT: S 19 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7557 (tpp-160) REVERT: V 43 ASP cc_start: 0.9309 (m-30) cc_final: 0.8773 (m-30) REVERT: V 52 ARG cc_start: 0.9297 (ttp80) cc_final: 0.8668 (ttp80) REVERT: Y 52 ARG cc_start: 0.9000 (ptp-110) cc_final: 0.8641 (mtm110) REVERT: e 10 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9069 (mmtp) REVERT: h 16 ASP cc_start: 0.8349 (t0) cc_final: 0.7698 (t0) REVERT: h 43 ASP cc_start: 0.8836 (m-30) cc_final: 0.8572 (OUTLIER) REVERT: h 52 ARG cc_start: 0.9205 (mtp-110) cc_final: 0.8722 (mtm-85) REVERT: k 54 LEU cc_start: 0.8953 (mm) cc_final: 0.8645 (pt) REVERT: n 3 GLU cc_start: 0.7327 (pp20) cc_final: 0.6958 (pm20) REVERT: n 11 LEU cc_start: 0.9754 (tp) cc_final: 0.9294 (pt) REVERT: n 16 ASP cc_start: 0.8426 (t0) cc_final: 0.7874 (t0) REVERT: n 56 LYS cc_start: 0.9001 (tppt) cc_final: 0.8719 (tppt) REVERT: q 10 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9114 (mmtp) REVERT: q 16 ASP cc_start: 0.8276 (t0) cc_final: 0.7723 (t0) REVERT: t 16 ASP cc_start: 0.8358 (t0) cc_final: 0.7789 (t0) REVERT: 3 16 ASP cc_start: 0.7958 (t0) cc_final: 0.7542 (t0) REVERT: 3 43 ASP cc_start: 0.9325 (m-30) cc_final: 0.9032 (m-30) REVERT: 6 16 ASP cc_start: 0.7841 (t0) cc_final: 0.7069 (t0) REVERT: 6 52 ARG cc_start: 0.8739 (ptp-110) cc_final: 0.8376 (ptt180) REVERT: G 36 VAL cc_start: 0.9578 (t) cc_final: 0.9296 (p) REVERT: Z 13 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: Z 17 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: i 30 LEU cc_start: 0.9778 (mt) cc_final: 0.9542 (mm) REVERT: o 36 VAL cc_start: 0.9718 (t) cc_final: 0.9444 (p) REVERT: r 16 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8738 (mttp) REVERT: r 52 LYS cc_start: 0.9386 (tppp) cc_final: 0.9180 (tppt) REVERT: u 36 VAL cc_start: 0.9515 (t) cc_final: 0.9180 (p) REVERT: 4 16 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8941 (ptpp) REVERT: d 21 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9231 (tm) REVERT: d 31 ILE cc_start: 0.9324 (tt) cc_final: 0.9108 (pp) REVERT: d 34 THR cc_start: 0.9448 (t) cc_final: 0.9137 (p) REVERT: p 34 THR cc_start: 0.9658 (t) cc_final: 0.9452 (p) REVERT: 5 16 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7522 (t0) outliers start: 98 outliers final: 41 residues processed: 616 average time/residue: 0.4774 time to fit residues: 374.5204 Evaluate side-chains 568 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 511 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 210 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain z residue 14 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain k residue 35 ILE Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 16 LYS Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 16 LYS Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain 5 residue 16 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 186 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN L 183 ASN z 46 ASN h 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.043034 restraints weight = 115549.207| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 4.34 r_work: 0.2517 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.909 33312 Z= 0.326 Angle : 1.046 18.737 46017 Z= 0.449 Chirality : 0.050 0.373 4813 Planarity : 0.005 0.054 5558 Dihedral : 16.621 179.545 5216 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.85 % Favored : 89.73 % Rotamer: Outliers : 3.18 % Allowed : 29.06 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.64 (0.15), residues: 3380 helix: 1.52 (0.12), residues: 1800 sheet: 0.09 (1.01), residues: 32 loop : -3.03 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG t 52 TYR 0.030 0.002 TYR V 27 PHE 0.034 0.002 PHE 7 22 TRP 0.028 0.002 TRP e 12 HIS 0.010 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00789 (33252) covalent geometry : angle 1.04565 (46017) hydrogen bonds : bond 0.05632 ( 1416) hydrogen bonds : angle 5.11974 ( 4125) Misc. bond : bond 0.14457 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 470 time to evaluate : 1.203 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: C 37 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8760 (mp10) REVERT: C 146 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8737 (mmm-85) REVERT: C 149 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: C 238 ASP cc_start: 0.9558 (t0) cc_final: 0.9199 (t0) REVERT: C 252 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.9019 (t) REVERT: L 23 ASP cc_start: 0.8960 (t0) cc_final: 0.8605 (t0) REVERT: L 60 ASP cc_start: 0.8981 (t0) cc_final: 0.8554 (t0) REVERT: L 106 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9110 (tp30) REVERT: L 127 MET cc_start: 0.9680 (tpp) cc_final: 0.9352 (tpp) REVERT: L 204 ASP cc_start: 0.9046 (m-30) cc_final: 0.8676 (m-30) REVERT: L 210 GLU cc_start: 0.9192 (mp0) cc_final: 0.8967 (mp0) REVERT: L 212 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9016 (pm20) REVERT: M 9 GLN cc_start: 0.9127 (mt0) cc_final: 0.8727 (mt0) REVERT: M 22 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8637 (tm-30) REVERT: M 26 ASN cc_start: 0.9642 (m-40) cc_final: 0.9352 (p0) REVERT: M 171 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9038 (mp0) REVERT: M 193 ASN cc_start: 0.9537 (t0) cc_final: 0.9091 (t0) REVERT: H 66 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: H 92 GLN cc_start: 0.9249 (pm20) cc_final: 0.8718 (pm20) REVERT: H 102 GLN cc_start: 0.8856 (mt0) cc_final: 0.8520 (pm20) REVERT: H 134 ILE cc_start: 0.9604 (mt) cc_final: 0.9284 (mm) REVERT: H 217 GLN cc_start: 0.9569 (mt0) cc_final: 0.8971 (mp10) REVERT: H 220 ASN cc_start: 0.9569 (m110) cc_final: 0.9205 (m-40) REVERT: K 16 ASP cc_start: 0.8612 (t0) cc_final: 0.7514 (t0) REVERT: K 18 ARG cc_start: 0.9183 (mtm110) cc_final: 0.8704 (tmt170) REVERT: K 43 ASP cc_start: 0.9290 (m-30) cc_final: 0.8676 (t0) REVERT: P 16 ASP cc_start: 0.8794 (t0) cc_final: 0.8015 (t0) REVERT: S 10 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.9315 (mmtp) REVERT: S 16 ASP cc_start: 0.8836 (t0) cc_final: 0.8316 (t0) REVERT: S 19 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7617 (tpp-160) REVERT: S 43 ASP cc_start: 0.9197 (m-30) cc_final: 0.8835 (t0) REVERT: V 43 ASP cc_start: 0.9437 (m-30) cc_final: 0.9089 (m-30) REVERT: V 52 ARG cc_start: 0.9282 (ttp80) cc_final: 0.8883 (ttp80) REVERT: e 10 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9030 (mmtp) REVERT: h 16 ASP cc_start: 0.8530 (t0) cc_final: 0.7877 (t0) REVERT: h 52 ARG cc_start: 0.9106 (mtp-110) cc_final: 0.8898 (mtp-110) REVERT: n 3 GLU cc_start: 0.7305 (pp20) cc_final: 0.6995 (pm20) REVERT: n 11 LEU cc_start: 0.9780 (tp) cc_final: 0.9306 (pt) REVERT: n 16 ASP cc_start: 0.8567 (t0) cc_final: 0.7997 (t0) REVERT: n 56 LYS cc_start: 0.9030 (tppt) cc_final: 0.8748 (tppt) REVERT: q 10 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9190 (mmtp) REVERT: q 15 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8900 (mm) REVERT: q 16 ASP cc_start: 0.8472 (t0) cc_final: 0.7910 (t0) REVERT: t 16 ASP cc_start: 0.8579 (t0) cc_final: 0.7978 (t0) REVERT: t 52 ARG cc_start: 0.9120 (mtm-85) cc_final: 0.8724 (mtm-85) REVERT: 3 16 ASP cc_start: 0.8166 (t0) cc_final: 0.7747 (t0) REVERT: 3 43 ASP cc_start: 0.9499 (m-30) cc_final: 0.9166 (m-30) REVERT: 6 16 ASP cc_start: 0.8084 (t0) cc_final: 0.7262 (t0) REVERT: Z 17 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: i 30 LEU cc_start: 0.9796 (mt) cc_final: 0.9561 (mm) REVERT: o 36 VAL cc_start: 0.9795 (t) cc_final: 0.9552 (p) REVERT: u 36 VAL cc_start: 0.9669 (t) cc_final: 0.9347 (p) REVERT: x 16 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8463 (pmmt) REVERT: 4 16 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9103 (ptpp) REVERT: U 23 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9122 (mm) REVERT: d 21 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9306 (tm) REVERT: d 34 THR cc_start: 0.9490 (t) cc_final: 0.9172 (p) REVERT: j 21 LEU cc_start: 0.9551 (mp) cc_final: 0.9331 (mm) REVERT: p 34 THR cc_start: 0.9600 (t) cc_final: 0.9356 (p) outliers start: 93 outliers final: 38 residues processed: 531 average time/residue: 0.5055 time to fit residues: 338.1897 Evaluate side-chains 499 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 443 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain f residue 28 LEU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 13 GLU Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 16 LYS Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain d residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 21 optimal weight: 1.9990 chunk 219 optimal weight: 0.0050 chunk 58 optimal weight: 0.0020 chunk 91 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 46 ASN h 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.046626 restraints weight = 111302.360| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.30 r_work: 0.2610 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.664 33312 Z= 0.160 Angle : 0.963 17.531 46017 Z= 0.414 Chirality : 0.046 0.307 4813 Planarity : 0.005 0.079 5558 Dihedral : 16.410 179.796 5216 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.25 % Favored : 91.42 % Rotamer: Outliers : 2.22 % Allowed : 30.05 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.65 (0.15), residues: 3380 helix: 1.53 (0.12), residues: 1777 sheet: 0.10 (0.99), residues: 32 loop : -2.99 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG S 52 TYR 0.031 0.001 TYR V 27 PHE 0.020 0.001 PHE L 235 TRP 0.025 0.002 TRP 2 30 HIS 0.004 0.001 HIS M 16 Details of bonding type rmsd covalent geometry : bond 0.00384 (33252) covalent geometry : angle 0.96313 (46017) hydrogen bonds : bond 0.04955 ( 1416) hydrogen bonds : angle 4.91616 ( 4125) Misc. bond : bond 0.09380 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 525 time to evaluate : 1.361 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: C 37 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: C 110 MET cc_start: 0.9669 (mmt) cc_final: 0.9017 (mmt) REVERT: C 146 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8732 (mmm-85) REVERT: C 149 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: C 188 ASP cc_start: 0.9218 (t0) cc_final: 0.8745 (t0) REVERT: C 233 MET cc_start: 0.9581 (mmp) cc_final: 0.8880 (mmt) REVERT: C 238 ASP cc_start: 0.9508 (t0) cc_final: 0.9152 (t0) REVERT: C 252 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8819 (p) REVERT: L 23 ASP cc_start: 0.8724 (t0) cc_final: 0.8422 (t0) REVERT: L 60 ASP cc_start: 0.8927 (t0) cc_final: 0.8461 (t0) REVERT: L 106 GLU cc_start: 0.9417 (tt0) cc_final: 0.9173 (tp30) REVERT: L 204 ASP cc_start: 0.9015 (m-30) cc_final: 0.8641 (m-30) REVERT: L 210 GLU cc_start: 0.9165 (mp0) cc_final: 0.8899 (mp0) REVERT: M 9 GLN cc_start: 0.9122 (mt0) cc_final: 0.8739 (mt0) REVERT: M 22 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8515 (tm-30) REVERT: M 26 ASN cc_start: 0.9613 (m-40) cc_final: 0.9364 (OUTLIER) REVERT: M 171 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9024 (mp0) REVERT: M 193 ASN cc_start: 0.9469 (t0) cc_final: 0.9038 (t0) REVERT: H 66 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: H 92 GLN cc_start: 0.9256 (pm20) cc_final: 0.8682 (pm20) REVERT: H 102 GLN cc_start: 0.8817 (mt0) cc_final: 0.8502 (pm20) REVERT: H 134 ILE cc_start: 0.9555 (mt) cc_final: 0.9272 (mm) REVERT: H 217 GLN cc_start: 0.9568 (mt0) cc_final: 0.9235 (mt0) REVERT: H 220 ASN cc_start: 0.9533 (m110) cc_final: 0.9162 (m-40) REVERT: F 29 THR cc_start: 0.9511 (m) cc_final: 0.9305 (m) REVERT: K 16 ASP cc_start: 0.8441 (t0) cc_final: 0.7305 (t0) REVERT: K 18 ARG cc_start: 0.9115 (mtm110) cc_final: 0.8680 (tmt170) REVERT: K 29 THR cc_start: 0.9652 (m) cc_final: 0.9233 (p) REVERT: K 43 ASP cc_start: 0.9208 (m-30) cc_final: 0.8837 (m-30) REVERT: P 16 ASP cc_start: 0.8636 (t0) cc_final: 0.7875 (t0) REVERT: S 10 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9404 (mmtp) REVERT: S 16 ASP cc_start: 0.8738 (t0) cc_final: 0.8206 (t0) REVERT: S 19 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7590 (tpp-160) REVERT: V 43 ASP cc_start: 0.9318 (m-30) cc_final: 0.8653 (m-30) REVERT: V 52 ARG cc_start: 0.9259 (ttp80) cc_final: 0.8680 (ttp80) REVERT: e 10 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9044 (mmtp) REVERT: h 16 ASP cc_start: 0.8456 (t0) cc_final: 0.7784 (t0) REVERT: n 3 GLU cc_start: 0.7350 (pp20) cc_final: 0.7113 (pm20) REVERT: n 11 LEU cc_start: 0.9753 (tp) cc_final: 0.9307 (pt) REVERT: n 16 ASP cc_start: 0.8365 (t0) cc_final: 0.7799 (t0) REVERT: n 56 LYS cc_start: 0.8985 (tppt) cc_final: 0.8704 (tppt) REVERT: q 10 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9182 (mmtp) REVERT: q 15 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8808 (mm) REVERT: q 16 ASP cc_start: 0.8387 (t0) cc_final: 0.7799 (t0) REVERT: t 16 ASP cc_start: 0.8374 (t0) cc_final: 0.7703 (t0) REVERT: 3 16 ASP cc_start: 0.8010 (t0) cc_final: 0.7591 (t0) REVERT: 3 43 ASP cc_start: 0.9375 (m-30) cc_final: 0.9085 (m-30) REVERT: 6 16 ASP cc_start: 0.7884 (t0) cc_final: 0.7043 (t0) REVERT: 6 52 ARG cc_start: 0.8678 (ptp-110) cc_final: 0.8284 (ptt90) REVERT: W 16 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8878 (mttm) REVERT: i 30 LEU cc_start: 0.9783 (mt) cc_final: 0.9560 (mm) REVERT: o 16 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8249 (mttm) REVERT: o 36 VAL cc_start: 0.9750 (t) cc_final: 0.9494 (p) REVERT: u 36 VAL cc_start: 0.9594 (t) cc_final: 0.9201 (p) REVERT: x 16 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8522 (ptpt) REVERT: 4 36 VAL cc_start: 0.9611 (t) cc_final: 0.9317 (p) REVERT: d 21 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9258 (tm) REVERT: d 34 THR cc_start: 0.9416 (t) cc_final: 0.9133 (p) REVERT: j 21 LEU cc_start: 0.9517 (mp) cc_final: 0.9313 (mm) REVERT: p 34 THR cc_start: 0.9608 (t) cc_final: 0.9357 (p) outliers start: 65 outliers final: 31 residues processed: 563 average time/residue: 0.4574 time to fit residues: 328.9561 Evaluate side-chains 550 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 505 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain v residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 128 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 178 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046457 restraints weight = 113201.573| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.23 r_work: 0.2622 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.666 33312 Z= 0.162 Angle : 0.962 17.661 46017 Z= 0.415 Chirality : 0.047 0.325 4813 Planarity : 0.005 0.090 5558 Dihedral : 16.246 179.819 5216 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.93 % Favored : 90.71 % Rotamer: Outliers : 1.84 % Allowed : 30.64 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.60 (0.15), residues: 3380 helix: 1.52 (0.12), residues: 1778 sheet: 0.13 (0.97), residues: 32 loop : -2.91 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG z 52 TYR 0.031 0.001 TYR V 27 PHE 0.032 0.001 PHE 7 22 TRP 0.046 0.002 TRP j 30 HIS 0.004 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00405 (33252) covalent geometry : angle 0.96169 (46017) hydrogen bonds : bond 0.04785 ( 1416) hydrogen bonds : angle 4.90939 ( 4125) Misc. bond : bond 0.09480 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 523 time to evaluate : 3.488 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: C 37 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8695 (mp10) REVERT: C 146 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8751 (mmm-85) REVERT: C 149 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: C 188 ASP cc_start: 0.9200 (t0) cc_final: 0.8699 (t0) REVERT: C 233 MET cc_start: 0.9600 (mmp) cc_final: 0.8892 (mmt) REVERT: C 238 ASP cc_start: 0.9512 (t0) cc_final: 0.9164 (t0) REVERT: C 252 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8753 (p) REVERT: L 23 ASP cc_start: 0.8728 (t0) cc_final: 0.8459 (t0) REVERT: L 60 ASP cc_start: 0.8940 (t0) cc_final: 0.8458 (t0) REVERT: L 106 GLU cc_start: 0.9406 (tt0) cc_final: 0.9105 (tp30) REVERT: L 127 MET cc_start: 0.9524 (tpp) cc_final: 0.9323 (tpp) REVERT: L 204 ASP cc_start: 0.9020 (m-30) cc_final: 0.8657 (m-30) REVERT: L 210 GLU cc_start: 0.9263 (mp0) cc_final: 0.9017 (mp0) REVERT: L 212 GLU cc_start: 0.9414 (pt0) cc_final: 0.9032 (pm20) REVERT: M 9 GLN cc_start: 0.9143 (mt0) cc_final: 0.8762 (mt0) REVERT: M 22 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8516 (tm-30) REVERT: M 26 ASN cc_start: 0.9624 (m-40) cc_final: 0.9419 (OUTLIER) REVERT: M 171 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.8988 (mp0) REVERT: M 193 ASN cc_start: 0.9450 (t0) cc_final: 0.9053 (t0) REVERT: H 66 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8373 (mtpp) REVERT: H 92 GLN cc_start: 0.9248 (pm20) cc_final: 0.8743 (pm20) REVERT: H 102 GLN cc_start: 0.8802 (mt0) cc_final: 0.8495 (pm20) REVERT: H 134 ILE cc_start: 0.9523 (mt) cc_final: 0.9244 (mm) REVERT: H 217 GLN cc_start: 0.9574 (mt0) cc_final: 0.9250 (mt0) REVERT: H 220 ASN cc_start: 0.9529 (m110) cc_final: 0.9174 (m-40) REVERT: K 16 ASP cc_start: 0.8470 (t0) cc_final: 0.7383 (t0) REVERT: K 18 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8698 (tmt170) REVERT: K 29 THR cc_start: 0.9657 (m) cc_final: 0.9247 (p) REVERT: K 43 ASP cc_start: 0.9213 (m-30) cc_final: 0.8858 (m-30) REVERT: P 16 ASP cc_start: 0.8543 (t0) cc_final: 0.7788 (t0) REVERT: P 52 ARG cc_start: 0.8867 (ptt180) cc_final: 0.8190 (mtm-85) REVERT: S 10 LYS cc_start: 0.9654 (OUTLIER) cc_final: 0.9399 (mmtp) REVERT: S 16 ASP cc_start: 0.8703 (t0) cc_final: 0.8167 (t0) REVERT: S 19 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7640 (tpp-160) REVERT: S 43 ASP cc_start: 0.8957 (m-30) cc_final: 0.8698 (t0) REVERT: V 43 ASP cc_start: 0.9261 (m-30) cc_final: 0.8905 (m-30) REVERT: V 52 ARG cc_start: 0.9261 (ttp80) cc_final: 0.8899 (ttp80) REVERT: b 56 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8685 (tptp) REVERT: e 10 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9085 (mmtp) REVERT: h 16 ASP cc_start: 0.8415 (t0) cc_final: 0.7751 (t0) REVERT: h 52 ARG cc_start: 0.9043 (mtp-110) cc_final: 0.8692 (mtm-85) REVERT: k 54 LEU cc_start: 0.8880 (mm) cc_final: 0.8564 (pt) REVERT: n 3 GLU cc_start: 0.7355 (pp20) cc_final: 0.7037 (pm20) REVERT: n 11 LEU cc_start: 0.9754 (tp) cc_final: 0.9296 (pt) REVERT: n 16 ASP cc_start: 0.8336 (t0) cc_final: 0.7772 (t0) REVERT: q 10 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9182 (mmtp) REVERT: q 15 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8831 (mm) REVERT: q 16 ASP cc_start: 0.8335 (t0) cc_final: 0.7754 (t0) REVERT: t 16 ASP cc_start: 0.8279 (t0) cc_final: 0.7621 (t0) REVERT: t 52 ARG cc_start: 0.9241 (mtp-110) cc_final: 0.8849 (mtm-85) REVERT: 3 16 ASP cc_start: 0.7969 (t0) cc_final: 0.7550 (t0) REVERT: 3 43 ASP cc_start: 0.9353 (m-30) cc_final: 0.9073 (m-30) REVERT: 6 16 ASP cc_start: 0.7814 (t0) cc_final: 0.7046 (t0) REVERT: 6 52 ARG cc_start: 0.8694 (ptp-110) cc_final: 0.8351 (ptt90) REVERT: W 16 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8874 (mttm) REVERT: i 30 LEU cc_start: 0.9782 (mt) cc_final: 0.9565 (mm) REVERT: o 16 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8286 (mttm) REVERT: o 36 VAL cc_start: 0.9753 (t) cc_final: 0.9497 (p) REVERT: u 36 VAL cc_start: 0.9604 (t) cc_final: 0.9289 (p) REVERT: 4 36 VAL cc_start: 0.9626 (t) cc_final: 0.9336 (p) REVERT: d 21 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9299 (tm) REVERT: d 34 THR cc_start: 0.9420 (t) cc_final: 0.9116 (p) REVERT: p 34 THR cc_start: 0.9622 (t) cc_final: 0.9375 (p) outliers start: 54 outliers final: 25 residues processed: 556 average time/residue: 0.4401 time to fit residues: 315.5827 Evaluate side-chains 544 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 505 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 52 ARG Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain b residue 56 LYS Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 15 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain v residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 98 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 174 optimal weight: 0.2980 chunk 122 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.047387 restraints weight = 112100.858| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.29 r_work: 0.2639 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.647 33312 Z= 0.162 Angle : 0.962 18.378 46017 Z= 0.413 Chirality : 0.047 0.339 4813 Planarity : 0.005 0.096 5558 Dihedral : 16.133 179.764 5216 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.70 % Favored : 91.01 % Rotamer: Outliers : 1.43 % Allowed : 31.45 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 aren not related in a simple way. whole: -0.61 (0.15), residues: 3380 helix: 1.55 (0.12), residues: 1761 sheet: 0.16 (0.95), residues: 32 loop : -2.92 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG S 52 TYR 0.034 0.001 TYR V 27 PHE 0.022 0.001 PHE 6 25 TRP 0.034 0.002 TRP j 30 HIS 0.004 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00403 (33252) covalent geometry : angle 0.96214 (46017) hydrogen bonds : bond 0.04706 ( 1416) hydrogen bonds : angle 4.91112 ( 4125) Misc. bond : bond 0.09165 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10509.11 seconds wall clock time: 179 minutes 59.33 seconds (10799.33 seconds total)