Starting phenix.real_space_refine on Wed Aug 27 00:03:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x02_37965/08_2025/8x02_37965.map" } resolution = 3.3 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= 0.008 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: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 27792 2.51 5 N 7968 2.21 5 O 8112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1840 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 3.28, per 1000 atoms: 0.07 Number of scatterers: 44160 At special positions: 0 Unit cell: (151.51, 151.51, 151.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 8112 8.00 N 7968 7.00 C 27792 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=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 42.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR A 119 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG C 15 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR C 119 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.513A pdb=" N LYS C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.654A pdb=" N GLN D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 44 " --> pdb=" O ASN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR D 119 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU D 231 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 48 removed outlier: 3.652A pdb=" N GLN E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET E 44 " --> pdb=" O ASN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 removed outlier: 4.015A pdb=" N THR E 119 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 removed outlier: 3.763A pdb=" N LEU E 231 " --> pdb=" O PRO E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG F 15 " --> pdb=" O ARG F 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN F 42 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR F 119 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET G 44 " --> pdb=" O ASN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR G 119 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG H 15 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET H 44 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR H 119 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 138 removed outlier: 3.511A pdb=" N LYS H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU H 231 " --> pdb=" O PRO H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG I 15 " --> pdb=" O ARG I 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN I 42 " --> pdb=" O MET I 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET I 44 " --> pdb=" O ASN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE I 66 " --> pdb=" O PHE I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 removed outlier: 4.017A pdb=" N THR I 119 " --> pdb=" O ASN I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL I 215 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 232 removed outlier: 3.763A pdb=" N LEU I 231 " --> pdb=" O PRO I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG J 15 " --> pdb=" O ARG J 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET J 44 " --> pdb=" O ASN J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE J 66 " --> pdb=" O PHE J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 120 removed outlier: 4.015A pdb=" N THR J 119 " --> pdb=" O ASN J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL J 215 " --> pdb=" O GLY J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU J 231 " --> pdb=" O PRO J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 48 removed outlier: 3.652A pdb=" N GLN K 42 " --> pdb=" O MET K 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET K 44 " --> pdb=" O ASN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE K 66 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 120 removed outlier: 4.015A pdb=" N THR K 119 " --> pdb=" O ASN K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL K 215 " --> pdb=" O GLY K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU K 231 " --> pdb=" O PRO K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG L 15 " --> pdb=" O ARG L 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN L 42 " --> pdb=" O MET L 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET L 44 " --> pdb=" O ASN L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR L 119 " --> pdb=" O ASN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU L 231 " --> pdb=" O PRO L 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET M 44 " --> pdb=" O ASN M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR M 119 " --> pdb=" O ASN M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL M 215 " --> pdb=" O GLY M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU M 231 " --> pdb=" O PRO M 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS N 27 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 48 removed outlier: 3.652A pdb=" N GLN N 42 " --> pdb=" O MET N 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET N 44 " --> pdb=" O ASN N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 57 Processing helix chain 'N' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR N 119 " --> pdb=" O ASN N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL N 215 " --> pdb=" O GLY N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 232 removed outlier: 3.763A pdb=" N LEU N 231 " --> pdb=" O PRO N 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 48 removed outlier: 3.652A pdb=" N GLN O 42 " --> pdb=" O MET O 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET O 44 " --> pdb=" O ASN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE O 66 " --> pdb=" O PHE O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR O 119 " --> pdb=" O ASN O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS O 138 " --> pdb=" O GLU O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL O 215 " --> pdb=" O GLY O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU O 231 " --> pdb=" O PRO O 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG P 15 " --> pdb=" O ARG P 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS P 21 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS P 27 " --> pdb=" O ALA P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN P 42 " --> pdb=" O MET P 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET P 44 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 Processing helix chain 'P' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR P 119 " --> pdb=" O ASN P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS P 138 " --> pdb=" O GLU P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL P 215 " --> pdb=" O GLY P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU P 231 " --> pdb=" O PRO P 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN Q 24 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET Q 44 " --> pdb=" O ASN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 57 Processing helix chain 'Q' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR Q 119 " --> pdb=" O ASN Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS Q 138 " --> pdb=" O GLU Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL Q 215 " --> pdb=" O GLY Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU Q 231 " --> pdb=" O PRO Q 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN R 42 " --> pdb=" O MET R 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 44 " --> pdb=" O ASN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 57 Processing helix chain 'R' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE R 66 " --> pdb=" O PHE R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 120 removed outlier: 4.017A pdb=" N THR R 119 " --> pdb=" O ASN R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS R 138 " --> pdb=" O GLU R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL R 215 " --> pdb=" O GLY R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU R 231 " --> pdb=" O PRO R 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN S 24 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN S 42 " --> pdb=" O MET S 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 57 Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE S 66 " --> pdb=" O PHE S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR S 119 " --> pdb=" O ASN S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS S 138 " --> pdb=" O GLU S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL S 215 " --> pdb=" O GLY S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 232 removed outlier: 3.763A pdb=" N LEU S 231 " --> pdb=" O PRO S 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG T 15 " --> pdb=" O ARG T 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN T 24 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN T 42 " --> pdb=" O MET T 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET T 44 " --> pdb=" O ASN T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 57 Processing helix chain 'T' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE T 66 " --> pdb=" O PHE T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR T 119 " --> pdb=" O ASN T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS T 138 " --> pdb=" O GLU T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL T 215 " --> pdb=" O GLY T 211 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 232 removed outlier: 3.763A pdb=" N LEU T 231 " --> pdb=" O PRO T 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG U 15 " --> pdb=" O ARG U 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN U 42 " --> pdb=" O MET U 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET U 44 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 57 Processing helix chain 'U' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE U 66 " --> pdb=" O PHE U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR U 119 " --> pdb=" O ASN U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS U 138 " --> pdb=" O GLU U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL U 215 " --> pdb=" O GLY U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU U 231 " --> pdb=" O PRO U 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG V 15 " --> pdb=" O ARG V 11 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS V 21 " --> pdb=" O ALA V 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS V 27 " --> pdb=" O ALA V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN V 42 " --> pdb=" O MET V 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET V 44 " --> pdb=" O ASN V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 57 Processing helix chain 'V' and resid 62 through 75 removed outlier: 3.653A pdb=" N PHE V 66 " --> pdb=" O PHE V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR V 119 " --> pdb=" O ASN V 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS V 138 " --> pdb=" O GLU V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 227 removed outlier: 3.871A pdb=" N VAL V 215 " --> pdb=" O GLY V 211 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU V 231 " --> pdb=" O PRO V 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 27 removed outlier: 3.540A pdb=" N ARG W 15 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS W 21 " --> pdb=" O ALA W 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN W 24 " --> pdb=" O LEU W 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS W 27 " --> pdb=" O ALA W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN W 42 " --> pdb=" O MET W 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET W 44 " --> pdb=" O ASN W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 57 Processing helix chain 'W' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE W 66 " --> pdb=" O PHE W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 116 through 120 removed outlier: 4.016A pdb=" N THR W 119 " --> pdb=" O ASN W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS W 138 " --> pdb=" O GLU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL W 215 " --> pdb=" O GLY W 211 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 232 removed outlier: 3.762A pdb=" N LEU W 231 " --> pdb=" O PRO W 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 27 removed outlier: 3.539A pdb=" N ARG X 15 " --> pdb=" O ARG X 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS X 21 " --> pdb=" O ALA X 17 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN X 24 " --> pdb=" O LEU X 20 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 48 removed outlier: 3.653A pdb=" N GLN X 42 " --> pdb=" O MET X 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET X 44 " --> pdb=" O ASN X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 57 Processing helix chain 'X' and resid 62 through 75 removed outlier: 3.654A pdb=" N PHE X 66 " --> pdb=" O PHE X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 116 through 120 removed outlier: 4.017A pdb=" N THR X 119 " --> pdb=" O ASN X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 138 removed outlier: 3.512A pdb=" N LYS X 138 " --> pdb=" O GLU X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 227 removed outlier: 3.872A pdb=" N VAL X 215 " --> pdb=" O GLY X 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 232 removed outlier: 3.761A pdb=" N LEU X 231 " --> pdb=" O PRO X 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 3.597A pdb=" N HIS A 5 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG A 184 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR A 199 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA A 180 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA A 201 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET A 178 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A 203 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU A 176 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP A 205 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA A 174 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 152 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET A 178 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A 154 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA A 180 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN A 155 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.609A pdb=" N HIS J 5 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.622A pdb=" N HIS B 5 " --> pdb=" O TYR T 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG B 184 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR B 199 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA B 180 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 201 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET B 178 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 203 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 176 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP B 205 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B 174 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 152 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET B 178 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER B 154 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA B 180 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN B 155 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.642A pdb=" N HIS N 5 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.620A pdb=" N HIS C 5 " --> pdb=" O TYR I 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG C 184 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR C 199 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA C 180 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 201 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET C 178 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR C 203 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU C 176 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP C 205 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA C 174 " --> pdb=" O ASP C 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR C 152 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET C 178 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER C 154 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA C 180 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN C 155 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.636A pdb=" N HIS F 5 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 3.673A pdb=" N HIS D 5 " --> pdb=" O TYR S 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 37 removed outlier: 3.532A pdb=" N ARG D 184 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR D 199 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA D 180 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA D 201 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET D 178 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR D 203 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D 176 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP D 205 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA D 174 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 152 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET D 178 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER D 154 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA D 180 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN D 155 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.649A pdb=" N HIS P 5 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.664A pdb=" N HIS E 5 " --> pdb=" O TYR R 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG E 184 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR E 199 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA E 180 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA E 201 " --> pdb=" O MET E 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET E 178 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR E 203 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU E 176 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP E 205 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA E 174 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR E 152 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET E 178 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER E 154 " --> pdb=" O MET E 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA E 180 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN E 155 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.616A pdb=" N HIS W 5 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG F 184 " --> pdb=" O ARG F 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR F 199 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA F 180 " --> pdb=" O TYR F 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA F 201 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET F 178 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR F 203 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU F 176 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP F 205 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA F 174 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR F 152 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET F 178 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER F 154 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA F 180 " --> pdb=" O SER F 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN F 155 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.629A pdb=" N HIS I 5 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.570A pdb=" N HIS G 5 " --> pdb=" O TYR K 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG G 184 " --> pdb=" O ARG G 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR G 199 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA G 180 " --> pdb=" O TYR G 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA G 201 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET G 178 " --> pdb=" O ALA G 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR G 203 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU G 176 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP G 205 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA G 174 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR G 152 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET G 178 " --> pdb=" O THR G 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER G 154 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA G 180 " --> pdb=" O SER G 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN G 155 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.644A pdb=" N HIS X 5 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.631A pdb=" N HIS H 5 " --> pdb=" O TYR J 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG H 184 " --> pdb=" O ARG H 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR H 199 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA H 180 " --> pdb=" O TYR H 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA H 201 " --> pdb=" O MET H 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET H 178 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR H 203 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU H 176 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP H 205 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA H 174 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR H 152 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET H 178 " --> pdb=" O THR H 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER H 154 " --> pdb=" O MET H 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA H 180 " --> pdb=" O SER H 154 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN H 155 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG I 184 " --> pdb=" O ARG I 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR I 199 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA I 180 " --> pdb=" O TYR I 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA I 201 " --> pdb=" O MET I 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET I 178 " --> pdb=" O ALA I 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR I 203 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU I 176 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP I 205 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA I 174 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR I 152 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET I 178 " --> pdb=" O THR I 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER I 154 " --> pdb=" O MET I 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA I 180 " --> pdb=" O SER I 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN I 155 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG J 184 " --> pdb=" O ARG J 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR J 199 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA J 180 " --> pdb=" O TYR J 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA J 201 " --> pdb=" O MET J 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET J 178 " --> pdb=" O ALA J 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR J 203 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU J 176 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP J 205 " --> pdb=" O ALA J 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA J 174 " --> pdb=" O ASP J 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR J 152 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET J 178 " --> pdb=" O THR J 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER J 154 " --> pdb=" O MET J 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA J 180 " --> pdb=" O SER J 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN J 155 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.670A pdb=" N HIS K 5 " --> pdb=" O TYR X 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG K 184 " --> pdb=" O ARG K 195 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR K 199 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA K 180 " --> pdb=" O TYR K 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA K 201 " --> pdb=" O MET K 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET K 178 " --> pdb=" O ALA K 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR K 203 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU K 176 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP K 205 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA K 174 " --> pdb=" O ASP K 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR K 152 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET K 178 " --> pdb=" O THR K 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER K 154 " --> pdb=" O MET K 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA K 180 " --> pdb=" O SER K 154 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN K 155 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'L' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG L 184 " --> pdb=" O ARG L 195 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR L 199 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA L 180 " --> pdb=" O TYR L 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA L 201 " --> pdb=" O MET L 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET L 178 " --> pdb=" O ALA L 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR L 203 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU L 176 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP L 205 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA L 174 " --> pdb=" O ASP L 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR L 152 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET L 178 " --> pdb=" O THR L 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER L 154 " --> pdb=" O MET L 178 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA L 180 " --> pdb=" O SER L 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN L 155 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 83 through 85 removed outlier: 3.626A pdb=" N HIS Q 5 " --> pdb=" O TYR L 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 4 through 8 removed outlier: 3.630A pdb=" N HIS M 5 " --> pdb=" O TYR O 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG M 184 " --> pdb=" O ARG M 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR M 199 " --> pdb=" O ALA M 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA M 180 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA M 201 " --> pdb=" O MET M 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET M 178 " --> pdb=" O ALA M 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR M 203 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU M 176 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP M 205 " --> pdb=" O ALA M 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA M 174 " --> pdb=" O ASP M 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR M 152 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET M 178 " --> pdb=" O THR M 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER M 154 " --> pdb=" O MET M 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA M 180 " --> pdb=" O SER M 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN M 155 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 83 through 85 removed outlier: 3.614A pdb=" N HIS U 5 " --> pdb=" O TYR M 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG N 184 " --> pdb=" O ARG N 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR N 199 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA N 180 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA N 201 " --> pdb=" O MET N 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET N 178 " --> pdb=" O ALA N 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR N 203 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU N 176 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP N 205 " --> pdb=" O ALA N 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA N 174 " --> pdb=" O ASP N 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR N 152 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET N 178 " --> pdb=" O THR N 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER N 154 " --> pdb=" O MET N 178 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA N 180 " --> pdb=" O SER N 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN N 155 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 83 through 85 removed outlier: 3.646A pdb=" N HIS T 5 " --> pdb=" O TYR N 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 6 through 8 Processing sheet with id=AD9, first strand: chain 'O' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG O 184 " --> pdb=" O ARG O 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR O 199 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA O 180 " --> pdb=" O TYR O 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA O 201 " --> pdb=" O MET O 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET O 178 " --> pdb=" O ALA O 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR O 203 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU O 176 " --> pdb=" O THR O 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP O 205 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA O 174 " --> pdb=" O ASP O 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR O 152 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET O 178 " --> pdb=" O THR O 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER O 154 " --> pdb=" O MET O 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA O 180 " --> pdb=" O SER O 154 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN O 155 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG P 184 " --> pdb=" O ARG P 195 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR P 199 " --> pdb=" O ALA P 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA P 180 " --> pdb=" O TYR P 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA P 201 " --> pdb=" O MET P 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET P 178 " --> pdb=" O ALA P 201 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR P 203 " --> pdb=" O LEU P 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU P 176 " --> pdb=" O THR P 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP P 205 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA P 174 " --> pdb=" O ASP P 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR P 152 " --> pdb=" O LEU P 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET P 178 " --> pdb=" O THR P 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER P 154 " --> pdb=" O MET P 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA P 180 " --> pdb=" O SER P 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN P 155 " --> pdb=" O ALA P 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 83 through 85 removed outlier: 3.645A pdb=" N HIS S 5 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 29 through 37 removed outlier: 3.534A pdb=" N ARG Q 184 " --> pdb=" O ARG Q 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR Q 199 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA Q 180 " --> pdb=" O TYR Q 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA Q 201 " --> pdb=" O MET Q 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET Q 178 " --> pdb=" O ALA Q 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR Q 203 " --> pdb=" O LEU Q 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU Q 176 " --> pdb=" O THR Q 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP Q 205 " --> pdb=" O ALA Q 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA Q 174 " --> pdb=" O ASP Q 205 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR Q 152 " --> pdb=" O LEU Q 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET Q 178 " --> pdb=" O THR Q 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER Q 154 " --> pdb=" O MET Q 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA Q 180 " --> pdb=" O SER Q 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN Q 155 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 83 through 85 Processing sheet with id=AE5, first strand: chain 'R' and resid 4 through 8 removed outlier: 3.634A pdb=" N HIS R 5 " --> pdb=" O TYR W 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG R 184 " --> pdb=" O ARG R 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR R 199 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA R 180 " --> pdb=" O TYR R 199 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA R 201 " --> pdb=" O MET R 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET R 178 " --> pdb=" O ALA R 201 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR R 203 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU R 176 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP R 205 " --> pdb=" O ALA R 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA R 174 " --> pdb=" O ASP R 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR R 152 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET R 178 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER R 154 " --> pdb=" O MET R 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA R 180 " --> pdb=" O SER R 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN R 155 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG S 184 " --> pdb=" O ARG S 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR S 199 " --> pdb=" O ALA S 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA S 180 " --> pdb=" O TYR S 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA S 201 " --> pdb=" O MET S 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET S 178 " --> pdb=" O ALA S 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR S 203 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU S 176 " --> pdb=" O THR S 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP S 205 " --> pdb=" O ALA S 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA S 174 " --> pdb=" O ASP S 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR S 152 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET S 178 " --> pdb=" O THR S 152 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER S 154 " --> pdb=" O MET S 178 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA S 180 " --> pdb=" O SER S 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN S 155 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG T 184 " --> pdb=" O ARG T 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR T 199 " --> pdb=" O ALA T 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA T 180 " --> pdb=" O TYR T 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA T 201 " --> pdb=" O MET T 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET T 178 " --> pdb=" O ALA T 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR T 203 " --> pdb=" O LEU T 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU T 176 " --> pdb=" O THR T 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP T 205 " --> pdb=" O ALA T 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA T 174 " --> pdb=" O ASP T 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR T 152 " --> pdb=" O LEU T 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET T 178 " --> pdb=" O THR T 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER T 154 " --> pdb=" O MET T 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA T 180 " --> pdb=" O SER T 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN T 155 " --> pdb=" O ALA T 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG U 184 " --> pdb=" O ARG U 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR U 199 " --> pdb=" O ALA U 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA U 180 " --> pdb=" O TYR U 199 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA U 201 " --> pdb=" O MET U 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET U 178 " --> pdb=" O ALA U 201 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR U 203 " --> pdb=" O LEU U 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU U 176 " --> pdb=" O THR U 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP U 205 " --> pdb=" O ALA U 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA U 174 " --> pdb=" O ASP U 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR U 152 " --> pdb=" O LEU U 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET U 178 " --> pdb=" O THR U 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER U 154 " --> pdb=" O MET U 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA U 180 " --> pdb=" O SER U 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN U 155 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 29 through 37 removed outlier: 3.534A pdb=" N ARG V 184 " --> pdb=" O ARG V 195 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR V 199 " --> pdb=" O ALA V 180 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA V 180 " --> pdb=" O TYR V 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA V 201 " --> pdb=" O MET V 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET V 178 " --> pdb=" O ALA V 201 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR V 203 " --> pdb=" O LEU V 176 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU V 176 " --> pdb=" O THR V 203 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP V 205 " --> pdb=" O ALA V 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA V 174 " --> pdb=" O ASP V 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR V 152 " --> pdb=" O LEU V 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET V 178 " --> pdb=" O THR V 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER V 154 " --> pdb=" O MET V 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA V 180 " --> pdb=" O SER V 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN V 155 " --> pdb=" O ALA V 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG W 184 " --> pdb=" O ARG W 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR W 199 " --> pdb=" O ALA W 180 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA W 180 " --> pdb=" O TYR W 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA W 201 " --> pdb=" O MET W 178 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N MET W 178 " --> pdb=" O ALA W 201 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR W 203 " --> pdb=" O LEU W 176 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU W 176 " --> pdb=" O THR W 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP W 205 " --> pdb=" O ALA W 174 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA W 174 " --> pdb=" O ASP W 205 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR W 152 " --> pdb=" O LEU W 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET W 178 " --> pdb=" O THR W 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER W 154 " --> pdb=" O MET W 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA W 180 " --> pdb=" O SER W 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN W 155 " --> pdb=" O ALA W 102 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 29 through 37 removed outlier: 3.533A pdb=" N ARG X 184 " --> pdb=" O ARG X 195 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR X 199 " --> pdb=" O ALA X 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA X 180 " --> pdb=" O TYR X 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA X 201 " --> pdb=" O MET X 178 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET X 178 " --> pdb=" O ALA X 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR X 203 " --> pdb=" O LEU X 176 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU X 176 " --> pdb=" O THR X 203 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP X 205 " --> pdb=" O ALA X 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA X 174 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR X 152 " --> pdb=" O LEU X 176 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET X 178 " --> pdb=" O THR X 152 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER X 154 " --> pdb=" O MET X 178 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA X 180 " --> pdb=" O SER X 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN X 155 " --> pdb=" O ALA X 102 " (cutoff:3.500A) 2037 hydrogen bonds defined for protein. 5679 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: 7.08 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14989 1.34 - 1.46: 5954 1.46 - 1.57: 23313 1.57 - 1.69: 0 1.69 - 1.81: 552 Bond restraints: 44808 Sorted by residual: bond pdb=" CB GLU B 35 " pdb=" CG GLU B 35 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB GLU E 35 " pdb=" CG GLU E 35 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB GLU S 35 " pdb=" CG GLU S 35 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CB GLU Q 35 " pdb=" CG GLU Q 35 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB GLU K 35 " pdb=" CG GLU K 35 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 44803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 57490 1.92 - 3.85: 2552 3.85 - 5.77: 198 5.77 - 7.69: 168 7.69 - 9.61: 24 Bond angle restraints: 60432 Sorted by residual: angle pdb=" N PRO C 170 " pdb=" CA PRO C 170 " pdb=" C PRO C 170 " ideal model delta sigma weight residual 110.70 117.35 -6.65 1.22e+00 6.72e-01 2.97e+01 angle pdb=" N PRO Q 170 " pdb=" CA PRO Q 170 " pdb=" C PRO Q 170 " ideal model delta sigma weight residual 110.70 117.35 -6.65 1.22e+00 6.72e-01 2.97e+01 angle pdb=" N PRO E 170 " pdb=" CA PRO E 170 " pdb=" C PRO E 170 " ideal model delta sigma weight residual 110.70 117.35 -6.65 1.22e+00 6.72e-01 2.97e+01 angle pdb=" N PRO B 170 " pdb=" CA PRO B 170 " pdb=" C PRO B 170 " ideal model delta sigma weight residual 110.70 117.35 -6.65 1.22e+00 6.72e-01 2.97e+01 angle pdb=" N PRO O 170 " pdb=" CA PRO O 170 " pdb=" C PRO O 170 " ideal model delta sigma weight residual 110.70 117.35 -6.65 1.22e+00 6.72e-01 2.97e+01 ... (remaining 60427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.28: 23977 9.28 - 18.56: 2735 18.56 - 27.84: 480 27.84 - 37.12: 408 37.12 - 46.40: 216 Dihedral angle restraints: 27816 sinusoidal: 11496 harmonic: 16320 Sorted by residual: dihedral pdb=" CA ASN J 169 " pdb=" C ASN J 169 " pdb=" N PRO J 170 " pdb=" CA PRO J 170 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN P 169 " pdb=" C ASN P 169 " pdb=" N PRO P 170 " pdb=" CA PRO P 170 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN V 169 " pdb=" C ASN V 169 " pdb=" N PRO V 170 " pdb=" CA PRO V 170 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 27813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4227 0.042 - 0.085: 1936 0.085 - 0.127: 577 0.127 - 0.169: 120 0.169 - 0.211: 124 Chirality restraints: 6984 Sorted by residual: chirality pdb=" CG LEU K 132 " pdb=" CB LEU K 132 " pdb=" CD1 LEU K 132 " pdb=" CD2 LEU K 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU V 132 " pdb=" CB LEU V 132 " pdb=" CD1 LEU V 132 " pdb=" CD2 LEU V 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU E 132 " pdb=" CB LEU E 132 " pdb=" CD1 LEU E 132 " pdb=" CD2 LEU E 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 6981 not shown) Planarity restraints: 7872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO O 170 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO O 171 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO O 171 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 171 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 170 " 0.049 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO G 171 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 171 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 171 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 170 " -0.049 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO N 171 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO N 171 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 171 " -0.041 5.00e-02 4.00e+02 ... (remaining 7869 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 13999 2.86 - 3.37: 38726 3.37 - 3.88: 67875 3.88 - 4.39: 76805 4.39 - 4.90: 134321 Nonbonded interactions: 331726 Sorted by model distance: nonbonded pdb=" OD1 ASP M 124 " pdb=" NH2 ARG M 127 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASP K 124 " pdb=" NH2 ARG K 127 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASP X 124 " pdb=" NH2 ARG X 127 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASP F 124 " pdb=" NH2 ARG F 127 " model vdw 2.355 3.120 nonbonded pdb=" OD1 ASP T 124 " pdb=" NH2 ARG T 127 " model vdw 2.355 3.120 ... (remaining 331721 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.430 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.007 0.054 44808 Z= 0.294 Angle : 0.970 9.614 60432 Z= 0.569 Chirality : 0.058 0.211 6984 Planarity : 0.008 0.073 7872 Dihedral : 10.257 46.397 17208 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.80 (0.09), residues: 5568 helix: -4.38 (0.05), residues: 2112 sheet: -2.60 (0.11), residues: 1200 loop : -1.95 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 184 TYR 0.015 0.003 TYR N 204 PHE 0.022 0.003 PHE F 163 HIS 0.005 0.002 HIS J 48 Details of bonding type rmsd covalent geometry : bond 0.00671 (44808) covalent geometry : angle 0.97011 (60432) hydrogen bonds : bond 0.35399 ( 2037) hydrogen bonds : angle 10.19762 ( 5679) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1152 time to evaluate : 1.444 Fit side-chains REVERT: A 7 GLU cc_start: 0.8055 (tp30) cc_final: 0.7783 (mt-10) REVERT: A 19 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7565 (mtp85) REVERT: A 70 SER cc_start: 0.9431 (m) cc_final: 0.9223 (m) REVERT: A 198 MET cc_start: 0.9086 (ttm) cc_final: 0.8771 (ttm) REVERT: B 19 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7451 (mtp85) REVERT: B 198 MET cc_start: 0.9093 (ttm) cc_final: 0.8783 (ttm) REVERT: C 19 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7502 (mtp85) REVERT: C 70 SER cc_start: 0.9438 (m) cc_final: 0.9219 (m) REVERT: C 198 MET cc_start: 0.9129 (ttm) cc_final: 0.8833 (ttm) REVERT: D 12 MET cc_start: 0.8110 (tpp) cc_final: 0.7605 (mtt) REVERT: D 19 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7446 (mtp85) REVERT: D 70 SER cc_start: 0.9437 (m) cc_final: 0.9226 (m) REVERT: E 12 MET cc_start: 0.8124 (tpp) cc_final: 0.7624 (mtt) REVERT: E 19 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7423 (mtp85) REVERT: E 70 SER cc_start: 0.9434 (m) cc_final: 0.9222 (m) REVERT: E 198 MET cc_start: 0.9137 (ttm) cc_final: 0.8841 (ttm) REVERT: F 19 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7462 (mtp85) REVERT: G 7 GLU cc_start: 0.7974 (tp30) cc_final: 0.7748 (mt-10) REVERT: G 19 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7555 (mtp85) REVERT: G 70 SER cc_start: 0.9437 (m) cc_final: 0.9223 (m) REVERT: G 198 MET cc_start: 0.9125 (ttm) cc_final: 0.8827 (ttm) REVERT: H 7 GLU cc_start: 0.8016 (tp30) cc_final: 0.7799 (mt-10) REVERT: H 19 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7504 (mtp85) REVERT: H 70 SER cc_start: 0.9434 (m) cc_final: 0.9215 (m) REVERT: H 198 MET cc_start: 0.9115 (ttm) cc_final: 0.8809 (ttm) REVERT: I 12 MET cc_start: 0.8202 (tpp) cc_final: 0.7709 (mtt) REVERT: I 19 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7411 (mtp85) REVERT: J 7 GLU cc_start: 0.8033 (tp30) cc_final: 0.7765 (mt-10) REVERT: J 19 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7534 (mtp85) REVERT: J 70 SER cc_start: 0.9426 (m) cc_final: 0.9219 (m) REVERT: J 198 MET cc_start: 0.9111 (ttm) cc_final: 0.8814 (ttm) REVERT: K 12 MET cc_start: 0.8130 (tpp) cc_final: 0.7619 (mtt) REVERT: K 19 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7410 (mtp85) REVERT: K 70 SER cc_start: 0.9428 (m) cc_final: 0.9212 (m) REVERT: K 198 MET cc_start: 0.9131 (ttm) cc_final: 0.8842 (ttm) REVERT: L 12 MET cc_start: 0.8195 (tpp) cc_final: 0.7705 (mtt) REVERT: L 19 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7492 (mtp85) REVERT: L 70 SER cc_start: 0.9423 (m) cc_final: 0.9213 (m) REVERT: L 198 MET cc_start: 0.9132 (ttm) cc_final: 0.8837 (ttm) REVERT: M 19 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7503 (mtp85) REVERT: M 70 SER cc_start: 0.9451 (m) cc_final: 0.9242 (m) REVERT: M 198 MET cc_start: 0.9123 (ttm) cc_final: 0.8824 (ttm) REVERT: N 19 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7487 (mtp85) REVERT: N 70 SER cc_start: 0.9442 (m) cc_final: 0.9222 (m) REVERT: N 198 MET cc_start: 0.9134 (ttm) cc_final: 0.8872 (ttm) REVERT: O 12 MET cc_start: 0.8207 (tpp) cc_final: 0.7696 (mtt) REVERT: O 19 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7398 (mtp85) REVERT: O 198 MET cc_start: 0.9117 (ttm) cc_final: 0.8811 (ttm) REVERT: P 19 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7343 (mtp85) REVERT: P 198 MET cc_start: 0.9108 (ttm) cc_final: 0.8843 (ttm) REVERT: Q 19 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7462 (mtp85) REVERT: R 19 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7470 (mtp85) REVERT: R 70 SER cc_start: 0.9419 (m) cc_final: 0.9207 (m) REVERT: S 19 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7382 (mtp85) REVERT: S 70 SER cc_start: 0.9439 (m) cc_final: 0.9219 (m) REVERT: T 19 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7512 (mtp85) REVERT: T 70 SER cc_start: 0.9434 (m) cc_final: 0.9230 (m) REVERT: T 198 MET cc_start: 0.9114 (ttm) cc_final: 0.8811 (ttm) REVERT: U 7 GLU cc_start: 0.8100 (tp30) cc_final: 0.7800 (mt-10) REVERT: U 19 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7584 (mtp85) REVERT: V 12 MET cc_start: 0.8132 (tpp) cc_final: 0.7623 (mtt) REVERT: V 19 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7774 (ttt90) REVERT: V 70 SER cc_start: 0.9442 (m) cc_final: 0.9221 (m) REVERT: W 19 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7560 (mtp85) REVERT: W 70 SER cc_start: 0.9441 (m) cc_final: 0.9229 (m) REVERT: W 198 MET cc_start: 0.9121 (ttm) cc_final: 0.8828 (ttm) REVERT: X 19 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7486 (mtp85) REVERT: X 70 SER cc_start: 0.9423 (m) cc_final: 0.9220 (m) REVERT: X 198 MET cc_start: 0.9095 (ttm) cc_final: 0.8783 (ttm) outliers start: 0 outliers final: 0 residues processed: 1152 average time/residue: 0.2603 time to fit residues: 459.9549 Evaluate side-chains 699 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 699 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 81 ASN A 155 ASN B 34 ASN B 81 ASN B 155 ASN C 34 ASN C 42 GLN C 81 ASN C 155 ASN D 34 ASN D 42 GLN D 81 ASN D 155 ASN E 34 ASN E 81 ASN E 155 ASN F 34 ASN F 42 GLN F 81 ASN F 155 ASN G 34 ASN G 81 ASN G 155 ASN H 34 ASN H 42 GLN H 81 ASN H 155 ASN I 34 ASN I 81 ASN I 155 ASN J 34 ASN J 81 ASN J 155 ASN K 34 ASN K 42 GLN K 81 ASN K 155 ASN L 34 ASN L 81 ASN L 155 ASN M 34 ASN M 42 GLN M 81 ASN M 155 ASN N 34 ASN N 81 ASN N 155 ASN O 34 ASN O 81 ASN O 155 ASN P 34 ASN P 42 GLN P 81 ASN P 155 ASN Q 34 ASN Q 81 ASN Q 155 ASN R 34 ASN R 42 GLN R 81 ASN R 155 ASN S 34 ASN S 42 GLN S 81 ASN S 155 ASN T 34 ASN T 42 GLN T 81 ASN T 155 ASN U 34 ASN U 81 ASN U 155 ASN V 34 ASN V 42 GLN V 81 ASN V 155 ASN W 34 ASN W 42 GLN W 81 ASN W 155 ASN X 34 ASN X 42 GLN X 81 ASN X 155 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092823 restraints weight = 61523.504| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.51 r_work: 0.2924 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 44808 Z= 0.143 Angle : 0.591 5.366 60432 Z= 0.327 Chirality : 0.047 0.138 6984 Planarity : 0.006 0.051 7872 Dihedral : 5.014 17.770 6168 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.31 % Allowed : 8.96 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.10), residues: 5568 helix: -1.97 (0.09), residues: 2040 sheet: -1.28 (0.13), residues: 1272 loop : -1.44 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 6 TYR 0.010 0.001 TYR J 199 PHE 0.011 0.002 PHE Q 66 HIS 0.002 0.001 HIS K 206 Details of bonding type rmsd covalent geometry : bond 0.00317 (44808) covalent geometry : angle 0.59118 (60432) hydrogen bonds : bond 0.05009 ( 2037) hydrogen bonds : angle 5.56211 ( 5679) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 808 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7409 (mtp85) REVERT: A 186 VAL cc_start: 0.8854 (t) cc_final: 0.8280 (m) REVERT: A 198 MET cc_start: 0.9481 (ttm) cc_final: 0.9191 (ttm) REVERT: B 19 ARG cc_start: 0.8034 (mtm180) cc_final: 0.7396 (mtp85) REVERT: B 186 VAL cc_start: 0.8850 (t) cc_final: 0.8271 (m) REVERT: B 198 MET cc_start: 0.9475 (ttm) cc_final: 0.9189 (ttm) REVERT: C 19 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7364 (mtp85) REVERT: C 198 MET cc_start: 0.9480 (ttm) cc_final: 0.9225 (ttm) REVERT: D 19 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7298 (mtp85) REVERT: E 19 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7363 (mtp85) REVERT: E 198 MET cc_start: 0.9474 (ttm) cc_final: 0.9211 (ttm) REVERT: F 19 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7391 (mtp85) REVERT: F 198 MET cc_start: 0.9483 (ttm) cc_final: 0.9216 (ttm) REVERT: G 7 GLU cc_start: 0.7958 (tp30) cc_final: 0.7647 (tp30) REVERT: G 19 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7414 (mtp85) REVERT: G 198 MET cc_start: 0.9466 (ttm) cc_final: 0.9229 (ttm) REVERT: H 19 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7390 (mtp85) REVERT: H 198 MET cc_start: 0.9469 (ttm) cc_final: 0.9204 (ttm) REVERT: I 19 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7360 (mtp85) REVERT: I 186 VAL cc_start: 0.8905 (t) cc_final: 0.8325 (m) REVERT: I 198 MET cc_start: 0.9464 (ttm) cc_final: 0.9163 (ttm) REVERT: J 19 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7400 (mtp85) REVERT: J 198 MET cc_start: 0.9448 (ttm) cc_final: 0.9208 (ttm) REVERT: K 19 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7344 (mtp85) REVERT: K 198 MET cc_start: 0.9468 (ttm) cc_final: 0.9206 (ttm) REVERT: L 19 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7354 (mtp85) REVERT: L 198 MET cc_start: 0.9493 (ttm) cc_final: 0.9241 (ttm) REVERT: M 19 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7398 (mtp85) REVERT: M 198 MET cc_start: 0.9467 (ttm) cc_final: 0.9206 (ttm) REVERT: N 19 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7361 (mtp85) REVERT: N 198 MET cc_start: 0.9468 (ttm) cc_final: 0.9210 (ttm) REVERT: O 19 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7325 (mtp85) REVERT: O 198 MET cc_start: 0.9493 (ttm) cc_final: 0.9231 (ttm) REVERT: P 19 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7292 (mtp85) REVERT: P 198 MET cc_start: 0.9466 (ttm) cc_final: 0.9202 (ttm) REVERT: Q 19 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7363 (mtp85) REVERT: Q 186 VAL cc_start: 0.8891 (t) cc_final: 0.8309 (m) REVERT: Q 198 MET cc_start: 0.9477 (ttm) cc_final: 0.9178 (ttm) REVERT: R 19 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7365 (mtp85) REVERT: R 198 MET cc_start: 0.9478 (ttm) cc_final: 0.9177 (ttm) REVERT: S 19 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7345 (mtp85) REVERT: T 19 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7438 (mtp85) REVERT: T 198 MET cc_start: 0.9480 (ttm) cc_final: 0.9218 (ttm) REVERT: U 19 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7406 (mtp85) REVERT: U 186 VAL cc_start: 0.8854 (t) cc_final: 0.8287 (m) REVERT: U 198 MET cc_start: 0.9472 (ttm) cc_final: 0.9180 (ttm) REVERT: V 19 ARG cc_start: 0.7982 (mtm180) cc_final: 0.7329 (mtp85) REVERT: W 19 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7415 (mtp85) REVERT: W 198 MET cc_start: 0.9478 (ttm) cc_final: 0.9219 (ttm) REVERT: X 19 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7361 (mtp85) REVERT: X 198 MET cc_start: 0.9484 (ttm) cc_final: 0.9181 (ttm) outliers start: 110 outliers final: 85 residues processed: 904 average time/residue: 0.2506 time to fit residues: 353.0229 Evaluate side-chains 697 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 612 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 383 optimal weight: 1.9990 chunk 426 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 237 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 433 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 285 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 42 GLN E 42 GLN G 42 GLN I 42 GLN J 42 GLN L 42 GLN N 42 GLN O 42 GLN Q 42 GLN Q 77 GLN U 42 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098498 restraints weight = 60493.922| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.43 r_work: 0.2976 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 44808 Z= 0.110 Angle : 0.548 7.975 60432 Z= 0.283 Chirality : 0.045 0.134 6984 Planarity : 0.005 0.041 7872 Dihedral : 4.439 13.359 6168 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.22 % Allowed : 11.85 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.10), residues: 5568 helix: -0.12 (0.10), residues: 2040 sheet: -0.84 (0.13), residues: 1296 loop : -1.14 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 6 TYR 0.007 0.001 TYR X 199 PHE 0.011 0.001 PHE S 66 HIS 0.002 0.001 HIS V 179 Details of bonding type rmsd covalent geometry : bond 0.00250 (44808) covalent geometry : angle 0.54825 (60432) hydrogen bonds : bond 0.03725 ( 2037) hydrogen bonds : angle 4.68284 ( 5679) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 681 time to evaluate : 1.693 Fit side-chains REVERT: A 7 GLU cc_start: 0.7973 (tp30) cc_final: 0.7671 (tp30) REVERT: A 19 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7386 (mtp85) REVERT: A 186 VAL cc_start: 0.8868 (t) cc_final: 0.8305 (m) REVERT: B 19 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7272 (mtp85) REVERT: B 186 VAL cc_start: 0.8872 (t) cc_final: 0.8305 (m) REVERT: C 19 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7291 (mtp85) REVERT: D 19 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7212 (mtp85) REVERT: E 19 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7235 (mtp85) REVERT: F 19 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7289 (mtp85) REVERT: F 220 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8743 (ttpp) REVERT: G 7 GLU cc_start: 0.7951 (tp30) cc_final: 0.7646 (tp30) REVERT: G 19 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7433 (mtp85) REVERT: G 120 MET cc_start: 0.8599 (mtt) cc_final: 0.8190 (mtp) REVERT: H 7 GLU cc_start: 0.7989 (tp30) cc_final: 0.7685 (tp30) REVERT: H 19 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7323 (mtp85) REVERT: I 19 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7256 (mtp85) REVERT: I 186 VAL cc_start: 0.8833 (t) cc_final: 0.8259 (m) REVERT: J 7 GLU cc_start: 0.7956 (tp30) cc_final: 0.7653 (tp30) REVERT: J 19 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7368 (mtp85) REVERT: J 220 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8733 (ttpp) REVERT: K 19 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7239 (mtp85) REVERT: L 19 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7566 (ttt90) REVERT: M 19 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7300 (mtp85) REVERT: M 120 MET cc_start: 0.8572 (mtt) cc_final: 0.8161 (mtp) REVERT: N 19 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7290 (mtp85) REVERT: O 19 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7255 (mtp85) REVERT: P 19 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7257 (mtp85) REVERT: Q 19 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7276 (mtp85) REVERT: Q 186 VAL cc_start: 0.8827 (t) cc_final: 0.8242 (m) REVERT: R 19 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7232 (mtp85) REVERT: R 220 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8735 (ttpp) REVERT: S 19 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7553 (ttt90) REVERT: T 19 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7580 (ttt90) REVERT: T 220 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8749 (ttpp) REVERT: U 7 GLU cc_start: 0.8022 (tp30) cc_final: 0.7662 (tp30) REVERT: U 19 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7383 (mtp85) REVERT: U 186 VAL cc_start: 0.8856 (t) cc_final: 0.8293 (m) REVERT: V 19 ARG cc_start: 0.7857 (mtm180) cc_final: 0.7234 (mtp85) REVERT: W 19 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7366 (mtp85) REVERT: X 19 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7271 (mtp85) outliers start: 153 outliers final: 126 residues processed: 806 average time/residue: 0.2243 time to fit residues: 292.8569 Evaluate side-chains 715 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 589 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 12 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 539 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095239 restraints weight = 61263.403| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.50 r_work: 0.2927 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 44808 Z= 0.154 Angle : 0.560 6.495 60432 Z= 0.294 Chirality : 0.046 0.152 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.464 14.775 6168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.45 % Allowed : 12.88 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.11), residues: 5568 helix: 0.52 (0.11), residues: 2064 sheet: -0.56 (0.13), residues: 1296 loop : -0.97 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 6 TYR 0.010 0.001 TYR S 199 PHE 0.021 0.002 PHE M 66 HIS 0.002 0.001 HIS P 179 Details of bonding type rmsd covalent geometry : bond 0.00374 (44808) covalent geometry : angle 0.55989 (60432) hydrogen bonds : bond 0.04033 ( 2037) hydrogen bonds : angle 4.54924 ( 5679) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 590 time to evaluate : 1.632 Fit side-chains REVERT: A 7 GLU cc_start: 0.7843 (tp30) cc_final: 0.7528 (tp30) REVERT: A 19 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7306 (mtp85) REVERT: A 186 VAL cc_start: 0.8942 (t) cc_final: 0.8409 (m) REVERT: B 7 GLU cc_start: 0.7737 (tp30) cc_final: 0.7353 (tp30) REVERT: B 19 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7133 (mtp85) REVERT: B 186 VAL cc_start: 0.8953 (t) cc_final: 0.8420 (m) REVERT: C 19 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7461 (ttt180) REVERT: D 19 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7451 (ttt180) REVERT: E 7 GLU cc_start: 0.7732 (tp30) cc_final: 0.7350 (tp30) REVERT: E 19 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7476 (ttt180) REVERT: E 93 TYR cc_start: 0.8786 (m-80) cc_final: 0.8492 (m-80) REVERT: F 19 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7178 (mtp85) REVERT: G 7 GLU cc_start: 0.7790 (tp30) cc_final: 0.7509 (tp30) REVERT: G 19 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7546 (ttt180) REVERT: H 7 GLU cc_start: 0.7869 (tp30) cc_final: 0.7575 (tp30) REVERT: H 19 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7461 (ttt180) REVERT: I 7 GLU cc_start: 0.7749 (tp30) cc_final: 0.7365 (tp30) REVERT: I 19 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7151 (mtp85) REVERT: I 186 VAL cc_start: 0.8969 (t) cc_final: 0.8415 (m) REVERT: J 7 GLU cc_start: 0.7845 (tp30) cc_final: 0.7528 (tp30) REVERT: J 19 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7523 (ttt180) REVERT: K 19 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7450 (ttt180) REVERT: L 19 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7456 (ttt180) REVERT: M 19 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7445 (ttt180) REVERT: N 19 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7483 (ttt180) REVERT: O 19 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7455 (ttt180) REVERT: P 7 GLU cc_start: 0.7747 (tp30) cc_final: 0.7347 (tp30) REVERT: P 19 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7193 (mtp85) REVERT: Q 19 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7174 (mtp85) REVERT: Q 186 VAL cc_start: 0.8939 (t) cc_final: 0.8421 (m) REVERT: R 19 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7121 (mtp85) REVERT: S 7 GLU cc_start: 0.7730 (tp30) cc_final: 0.7331 (tp30) REVERT: S 19 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7177 (mtp85) REVERT: T 7 GLU cc_start: 0.7733 (tp30) cc_final: 0.7329 (tp30) REVERT: T 19 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7260 (mtp85) REVERT: U 19 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7530 (ttt180) REVERT: U 186 VAL cc_start: 0.8941 (t) cc_final: 0.8408 (m) REVERT: V 19 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7463 (ttt180) REVERT: W 19 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7498 (ttt180) REVERT: X 19 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7108 (mtp85) outliers start: 164 outliers final: 160 residues processed: 702 average time/residue: 0.2567 time to fit residues: 288.0981 Evaluate side-chains 733 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 573 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 57 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 395 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096236 restraints weight = 61045.450| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.49 r_work: 0.2938 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 44808 Z= 0.131 Angle : 0.522 6.430 60432 Z= 0.273 Chirality : 0.045 0.141 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.286 13.497 6168 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.94 % Allowed : 15.19 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.11), residues: 5568 helix: 1.07 (0.11), residues: 2040 sheet: -0.35 (0.12), residues: 1560 loop : -1.18 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 6 TYR 0.008 0.001 TYR H 199 PHE 0.013 0.002 PHE I 66 HIS 0.002 0.001 HIS T 5 Details of bonding type rmsd covalent geometry : bond 0.00317 (44808) covalent geometry : angle 0.52163 (60432) hydrogen bonds : bond 0.03515 ( 2037) hydrogen bonds : angle 4.34965 ( 5679) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 634 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7542 (ttt180) REVERT: A 186 VAL cc_start: 0.9001 (t) cc_final: 0.8464 (m) REVERT: B 7 GLU cc_start: 0.7792 (tp30) cc_final: 0.7367 (tp30) REVERT: B 19 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7492 (ttt180) REVERT: B 178 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8672 (ptm) REVERT: B 186 VAL cc_start: 0.8996 (t) cc_final: 0.8452 (m) REVERT: C 19 ARG cc_start: 0.7913 (mtm180) cc_final: 0.7532 (ttt180) REVERT: D 19 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7470 (ttt180) REVERT: E 7 GLU cc_start: 0.7775 (tp30) cc_final: 0.7353 (tp30) REVERT: E 19 ARG cc_start: 0.7857 (mtm180) cc_final: 0.7478 (ttt180) REVERT: E 93 TYR cc_start: 0.8841 (m-80) cc_final: 0.8485 (m-80) REVERT: F 19 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7191 (mtp85) REVERT: G 19 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7578 (ttt180) REVERT: H 7 GLU cc_start: 0.7783 (tp30) cc_final: 0.7497 (tp30) REVERT: H 19 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7480 (ttt180) REVERT: I 7 GLU cc_start: 0.7788 (tp30) cc_final: 0.7360 (tp30) REVERT: I 19 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7054 (mtp85) REVERT: I 178 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8776 (ptm) REVERT: I 186 VAL cc_start: 0.8993 (t) cc_final: 0.8470 (m) REVERT: J 19 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7536 (ttt180) REVERT: J 178 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8716 (ptm) REVERT: K 19 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7481 (ttt180) REVERT: L 19 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7481 (ttt180) REVERT: L 178 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: M 19 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7470 (ttt180) REVERT: M 178 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8929 (ptm) REVERT: N 19 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7472 (ttt180) REVERT: N 93 TYR cc_start: 0.8831 (m-80) cc_final: 0.8502 (m-80) REVERT: O 19 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7501 (ttt180) REVERT: O 178 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8772 (ptm) REVERT: P 19 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7171 (mtp85) REVERT: P 178 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8924 (ptm) REVERT: Q 19 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7480 (ttt180) REVERT: Q 178 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8721 (ptm) REVERT: Q 186 VAL cc_start: 0.8974 (t) cc_final: 0.8464 (m) REVERT: R 19 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7478 (ttt180) REVERT: R 178 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8702 (ptm) REVERT: S 19 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7180 (mtp85) REVERT: T 19 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7498 (ttt180) REVERT: T 178 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8807 (ptm) REVERT: U 19 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7541 (ttt180) REVERT: U 75 GLN cc_start: 0.9102 (tt0) cc_final: 0.8875 (tt0) REVERT: U 178 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8713 (ptm) REVERT: U 186 VAL cc_start: 0.8994 (t) cc_final: 0.8450 (m) REVERT: V 19 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7498 (ttt180) REVERT: V 75 GLN cc_start: 0.9105 (tt0) cc_final: 0.8879 (tt0) REVERT: W 7 GLU cc_start: 0.7866 (tp30) cc_final: 0.7496 (tp30) REVERT: W 19 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7547 (ttt180) REVERT: X 19 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7443 (ttt180) outliers start: 187 outliers final: 148 residues processed: 775 average time/residue: 0.3102 time to fit residues: 374.3573 Evaluate side-chains 786 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 627 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 363 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 527 optimal weight: 0.9990 chunk 268 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 456 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097204 restraints weight = 60891.365| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.48 r_work: 0.2948 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44808 Z= 0.116 Angle : 0.508 6.414 60432 Z= 0.266 Chirality : 0.044 0.136 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.162 12.244 6168 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.64 % Allowed : 15.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.11), residues: 5568 helix: 1.45 (0.11), residues: 2040 sheet: -0.27 (0.12), residues: 1560 loop : -1.13 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 6 TYR 0.007 0.001 TYR S 199 PHE 0.010 0.001 PHE K 66 HIS 0.002 0.001 HIS U 5 Details of bonding type rmsd covalent geometry : bond 0.00278 (44808) covalent geometry : angle 0.50811 (60432) hydrogen bonds : bond 0.03247 ( 2037) hydrogen bonds : angle 4.26694 ( 5679) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 655 time to evaluate : 1.637 Fit side-chains REVERT: A 19 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7532 (ttt180) REVERT: A 107 ARG cc_start: 0.6349 (tmm160) cc_final: 0.6146 (tmm160) REVERT: A 186 VAL cc_start: 0.8965 (t) cc_final: 0.8419 (m) REVERT: B 19 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7238 (mtp85) REVERT: B 107 ARG cc_start: 0.6345 (tmm160) cc_final: 0.6144 (tmm160) REVERT: B 154 SER cc_start: 0.9258 (t) cc_final: 0.9002 (p) REVERT: B 178 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8641 (ptm) REVERT: B 186 VAL cc_start: 0.8964 (t) cc_final: 0.8416 (m) REVERT: C 19 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7543 (ttt180) REVERT: C 75 GLN cc_start: 0.9099 (tt0) cc_final: 0.8876 (tt0) REVERT: C 107 ARG cc_start: 0.6294 (tmm160) cc_final: 0.6088 (tmm160) REVERT: C 178 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8927 (ptm) REVERT: D 19 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7471 (ttt180) REVERT: D 178 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8870 (ptm) REVERT: E 19 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7173 (mtp85) REVERT: E 93 TYR cc_start: 0.8832 (m-80) cc_final: 0.8463 (m-80) REVERT: E 107 ARG cc_start: 0.6294 (tmm160) cc_final: 0.6074 (tmm160) REVERT: E 178 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8886 (ptm) REVERT: F 19 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7225 (mtp85) REVERT: G 19 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7563 (ttt180) REVERT: G 75 GLN cc_start: 0.9077 (tt0) cc_final: 0.8866 (tt0) REVERT: G 107 ARG cc_start: 0.6329 (tmm160) cc_final: 0.6118 (tmm160) REVERT: G 154 SER cc_start: 0.9253 (t) cc_final: 0.9006 (p) REVERT: G 178 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8859 (ptm) REVERT: H 7 GLU cc_start: 0.7812 (tp30) cc_final: 0.7505 (tp30) REVERT: H 19 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7527 (ttt180) REVERT: H 75 GLN cc_start: 0.9082 (tt0) cc_final: 0.8866 (tt0) REVERT: H 93 TYR cc_start: 0.8857 (m-80) cc_final: 0.8487 (m-80) REVERT: H 107 ARG cc_start: 0.6354 (tmm160) cc_final: 0.6143 (tmm160) REVERT: H 178 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8799 (ptm) REVERT: I 19 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7431 (ttt180) REVERT: I 107 ARG cc_start: 0.6352 (tmm160) cc_final: 0.6151 (tmm160) REVERT: I 178 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8698 (ptm) REVERT: I 186 VAL cc_start: 0.8968 (t) cc_final: 0.8438 (m) REVERT: J 19 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7529 (ttt180) REVERT: J 178 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8716 (ptm) REVERT: K 19 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7489 (ttt180) REVERT: K 178 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8804 (ptm) REVERT: L 19 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7455 (ttt180) REVERT: L 178 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8732 (ptm) REVERT: M 19 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7504 (ttt180) REVERT: M 75 GLN cc_start: 0.9101 (tt0) cc_final: 0.8885 (tt0) REVERT: M 178 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8868 (ptm) REVERT: N 19 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7199 (mtp85) REVERT: N 75 GLN cc_start: 0.9093 (tt0) cc_final: 0.8879 (tt0) REVERT: N 178 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8943 (ptm) REVERT: O 19 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7489 (ttt180) REVERT: O 107 ARG cc_start: 0.6322 (tmm160) cc_final: 0.6119 (tmm160) REVERT: O 178 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8718 (ptm) REVERT: P 19 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7148 (mtp85) REVERT: P 75 GLN cc_start: 0.9105 (tt0) cc_final: 0.8893 (tt0) REVERT: P 107 ARG cc_start: 0.6325 (tmm160) cc_final: 0.6123 (tmm160) REVERT: P 178 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8835 (ptm) REVERT: Q 19 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7233 (mtp85) REVERT: Q 154 SER cc_start: 0.9249 (t) cc_final: 0.9007 (p) REVERT: Q 178 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8704 (ptm) REVERT: Q 186 VAL cc_start: 0.8970 (t) cc_final: 0.8429 (m) REVERT: R 19 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7501 (ttt180) REVERT: R 107 ARG cc_start: 0.6352 (tmm160) cc_final: 0.6152 (tmm160) REVERT: R 178 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8652 (ptm) REVERT: S 19 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7498 (ttt180) REVERT: S 107 ARG cc_start: 0.6314 (tmm160) cc_final: 0.6101 (tmm160) REVERT: S 178 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8933 (ptm) REVERT: T 19 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7532 (ttt180) REVERT: T 178 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8702 (ptm) REVERT: U 19 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7539 (ttt180) REVERT: U 75 GLN cc_start: 0.9073 (tt0) cc_final: 0.8865 (tt0) REVERT: U 107 ARG cc_start: 0.6425 (tmm160) cc_final: 0.6214 (tmm160) REVERT: U 178 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8621 (ptm) REVERT: U 186 VAL cc_start: 0.8965 (t) cc_final: 0.8420 (m) REVERT: V 19 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7194 (mtp85) REVERT: V 178 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8891 (ptm) REVERT: W 7 GLU cc_start: 0.7851 (tp30) cc_final: 0.7428 (tp30) REVERT: W 19 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7538 (ttt180) REVERT: W 75 GLN cc_start: 0.9097 (tt0) cc_final: 0.8876 (tt0) REVERT: W 178 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8843 (ptm) REVERT: X 19 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7501 (ttt180) REVERT: X 107 ARG cc_start: 0.6410 (tmm160) cc_final: 0.6204 (tmm160) outliers start: 173 outliers final: 142 residues processed: 785 average time/residue: 0.2530 time to fit residues: 312.2662 Evaluate side-chains 790 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 627 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 267 optimal weight: 5.9990 chunk 454 optimal weight: 3.9990 chunk 328 optimal weight: 0.0060 chunk 161 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 420 optimal weight: 6.9990 chunk 521 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 470 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 40 ASN A 206 HIS B 40 ASN B 206 HIS C 40 ASN D 40 ASN E 40 ASN F 40 ASN F 206 HIS G 40 ASN G 206 HIS H 40 ASN H 206 HIS I 40 ASN I 206 HIS J 5 HIS J 40 ASN J 206 HIS K 40 ASN K 206 HIS L 40 ASN L 77 GLN M 40 ASN M 206 HIS N 40 ASN O 40 ASN O 206 HIS P 5 HIS P 40 ASN Q 40 ASN R 40 ASN R 206 HIS S 5 HIS S 40 ASN T 40 ASN T 206 HIS U 40 ASN V 40 ASN W 40 ASN W 206 HIS X 40 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.090721 restraints weight = 60967.724| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.50 r_work: 0.2884 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 44808 Z= 0.197 Angle : 0.577 6.500 60432 Z= 0.304 Chirality : 0.046 0.164 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.546 15.849 6168 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.66 % Allowed : 16.18 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.11), residues: 5568 helix: 1.17 (0.11), residues: 2064 sheet: -0.29 (0.12), residues: 1560 loop : -1.18 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 6 TYR 0.011 0.001 TYR S 199 PHE 0.019 0.002 PHE O 66 HIS 0.004 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00486 (44808) covalent geometry : angle 0.57739 (60432) hydrogen bonds : bond 0.04274 ( 2037) hydrogen bonds : angle 4.47925 ( 5679) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 627 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.9002 (t) cc_final: 0.8533 (m) REVERT: B 186 VAL cc_start: 0.8986 (t) cc_final: 0.8525 (m) REVERT: D 19 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7353 (ttt180) REVERT: I 186 VAL cc_start: 0.8978 (t) cc_final: 0.8531 (m) REVERT: K 19 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7364 (ttt180) REVERT: L 7 GLU cc_start: 0.7181 (mp0) cc_final: 0.6873 (mt-10) REVERT: L 19 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7367 (ttt180) REVERT: O 19 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7362 (ttt180) REVERT: Q 19 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7415 (ttt180) REVERT: Q 186 VAL cc_start: 0.8999 (t) cc_final: 0.8548 (m) REVERT: S 19 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7448 (ttt180) REVERT: U 186 VAL cc_start: 0.8999 (t) cc_final: 0.8536 (m) REVERT: V 19 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7383 (ttt180) REVERT: W 7 GLU cc_start: 0.7815 (tp30) cc_final: 0.7338 (tp30) outliers start: 174 outliers final: 172 residues processed: 776 average time/residue: 0.2490 time to fit residues: 303.0493 Evaluate side-chains 779 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 607 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 368 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 410 optimal weight: 0.7980 chunk 470 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 326 optimal weight: 0.9990 chunk 499 optimal weight: 0.0070 chunk 56 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 HIS E 5 HIS I 5 HIS L 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.089416 restraints weight = 60790.070| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.72 r_work: 0.2794 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 44808 Z= 0.154 Angle : 0.555 6.504 60432 Z= 0.289 Chirality : 0.046 0.164 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.413 14.676 6168 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.39 % Allowed : 16.54 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.11), residues: 5568 helix: 1.39 (0.11), residues: 2064 sheet: -0.31 (0.12), residues: 1560 loop : -1.10 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 219 TYR 0.009 0.001 TYR P 199 PHE 0.014 0.002 PHE C 66 HIS 0.003 0.001 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00378 (44808) covalent geometry : angle 0.55528 (60432) hydrogen bonds : bond 0.03752 ( 2037) hydrogen bonds : angle 4.39288 ( 5679) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 613 time to evaluate : 1.463 Fit side-chains REVERT: A 186 VAL cc_start: 0.8996 (t) cc_final: 0.8536 (m) REVERT: B 186 VAL cc_start: 0.9002 (t) cc_final: 0.8544 (m) REVERT: D 19 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7420 (ttt180) REVERT: D 154 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9123 (p) REVERT: I 186 VAL cc_start: 0.9005 (t) cc_final: 0.8518 (m) REVERT: K 19 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7456 (ttt180) REVERT: K 154 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9119 (p) REVERT: L 7 GLU cc_start: 0.7305 (mp0) cc_final: 0.6935 (mt-10) REVERT: L 19 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7420 (ttt180) REVERT: O 19 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7467 (ttt180) REVERT: P 154 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.9122 (p) REVERT: Q 19 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7458 (ttt180) REVERT: Q 186 VAL cc_start: 0.8959 (t) cc_final: 0.8514 (m) REVERT: S 19 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7478 (ttt180) REVERT: S 154 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9112 (p) REVERT: U 186 VAL cc_start: 0.8996 (t) cc_final: 0.8530 (m) REVERT: V 19 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7481 (ttt180) REVERT: W 7 GLU cc_start: 0.7835 (tp30) cc_final: 0.7495 (tp30) outliers start: 161 outliers final: 153 residues processed: 750 average time/residue: 0.2523 time to fit residues: 300.4184 Evaluate side-chains 766 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 609 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 372 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 439 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 435 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.090735 restraints weight = 59410.124| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.74 r_work: 0.2772 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44808 Z= 0.115 Angle : 0.524 6.509 60432 Z= 0.272 Chirality : 0.045 0.158 6984 Planarity : 0.004 0.040 7872 Dihedral : 4.136 12.252 6168 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.43 % Allowed : 16.31 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.11), residues: 5568 helix: 1.91 (0.11), residues: 2040 sheet: -0.23 (0.12), residues: 1560 loop : -1.01 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 219 TYR 0.006 0.001 TYR S 199 PHE 0.009 0.001 PHE T 66 HIS 0.002 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00275 (44808) covalent geometry : angle 0.52399 (60432) hydrogen bonds : bond 0.03088 ( 2037) hydrogen bonds : angle 4.21230 ( 5679) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 617 time to evaluate : 1.708 Fit side-chains REVERT: A 154 SER cc_start: 0.9131 (t) cc_final: 0.8876 (p) REVERT: A 186 VAL cc_start: 0.8907 (t) cc_final: 0.8331 (m) REVERT: B 154 SER cc_start: 0.9151 (t) cc_final: 0.8879 (p) REVERT: B 178 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8621 (ptm) REVERT: B 186 VAL cc_start: 0.8908 (t) cc_final: 0.8334 (m) REVERT: C 154 SER cc_start: 0.9175 (t) cc_final: 0.8901 (p) REVERT: C 178 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8756 (ptm) REVERT: D 19 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7468 (ttt180) REVERT: D 154 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9073 (p) REVERT: D 178 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8744 (ptm) REVERT: E 154 SER cc_start: 0.9165 (t) cc_final: 0.8908 (p) REVERT: E 178 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8809 (ptm) REVERT: F 154 SER cc_start: 0.9163 (t) cc_final: 0.8909 (p) REVERT: G 154 SER cc_start: 0.9146 (t) cc_final: 0.8896 (p) REVERT: G 178 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8790 (ptm) REVERT: H 178 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8732 (ptm) REVERT: I 154 SER cc_start: 0.9145 (t) cc_final: 0.8887 (p) REVERT: I 178 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8570 (ptm) REVERT: I 186 VAL cc_start: 0.8927 (t) cc_final: 0.8360 (m) REVERT: J 154 SER cc_start: 0.9145 (t) cc_final: 0.8893 (p) REVERT: J 178 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8642 (ptm) REVERT: K 19 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7374 (ttt180) REVERT: K 154 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.9073 (p) REVERT: K 178 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8756 (ptm) REVERT: L 19 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7350 (ttt180) REVERT: L 154 SER cc_start: 0.9148 (t) cc_final: 0.8889 (p) REVERT: L 178 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8659 (ptm) REVERT: M 154 SER cc_start: 0.9138 (t) cc_final: 0.8876 (p) REVERT: M 178 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8782 (ptm) REVERT: N 178 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8758 (ptm) REVERT: O 19 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7392 (ttt180) REVERT: O 154 SER cc_start: 0.9133 (t) cc_final: 0.8869 (p) REVERT: O 178 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8644 (ptm) REVERT: P 178 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8775 (ptm) REVERT: Q 19 ARG cc_start: 0.7873 (mtm180) cc_final: 0.7407 (ttt180) REVERT: Q 126 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8325 (mm-30) REVERT: Q 154 SER cc_start: 0.9132 (t) cc_final: 0.8871 (p) REVERT: Q 178 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8625 (ptm) REVERT: Q 186 VAL cc_start: 0.8948 (t) cc_final: 0.8397 (m) REVERT: R 154 SER cc_start: 0.9154 (t) cc_final: 0.8885 (p) REVERT: R 178 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8640 (ptm) REVERT: S 19 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7454 (ttt180) REVERT: S 178 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8828 (ptm) REVERT: T 178 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8608 (ptm) REVERT: U 178 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8593 (ptm) REVERT: U 186 VAL cc_start: 0.8915 (t) cc_final: 0.8339 (m) REVERT: V 19 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7378 (ttt180) REVERT: V 178 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8765 (ptm) REVERT: W 178 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8773 (ptm) REVERT: X 154 SER cc_start: 0.9145 (t) cc_final: 0.8888 (p) outliers start: 163 outliers final: 131 residues processed: 755 average time/residue: 0.2611 time to fit residues: 313.0523 Evaluate side-chains 761 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 607 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 282 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 469 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 295 optimal weight: 0.9990 chunk 403 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 40 ASN E 40 ASN H 40 ASN I 40 ASN L 40 ASN L 77 GLN M 40 ASN O 40 ASN P 40 ASN Q 40 ASN R 40 ASN T 40 ASN U 40 ASN V 40 ASN W 40 ASN X 40 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.090526 restraints weight = 59763.033| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.72 r_work: 0.2783 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44808 Z= 0.117 Angle : 0.526 6.495 60432 Z= 0.273 Chirality : 0.045 0.159 6984 Planarity : 0.004 0.041 7872 Dihedral : 4.085 12.896 6168 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.54 % Allowed : 16.06 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5568 helix: 2.19 (0.11), residues: 2040 sheet: -0.18 (0.12), residues: 1560 loop : -0.96 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 219 TYR 0.006 0.001 TYR O 199 PHE 0.010 0.001 PHE X 66 HIS 0.004 0.001 HIS H 5 Details of bonding type rmsd covalent geometry : bond 0.00281 (44808) covalent geometry : angle 0.52589 (60432) hydrogen bonds : bond 0.03108 ( 2037) hydrogen bonds : angle 4.18263 ( 5679) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11136 Ramachandran restraints generated. 5568 Oldfield, 0 Emsley, 5568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 626 time to evaluate : 1.744 Fit side-chains REVERT: A 154 SER cc_start: 0.9125 (t) cc_final: 0.8867 (p) REVERT: A 186 VAL cc_start: 0.8916 (t) cc_final: 0.8343 (m) REVERT: B 154 SER cc_start: 0.9150 (t) cc_final: 0.8879 (p) REVERT: B 178 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8619 (ptm) REVERT: B 186 VAL cc_start: 0.8885 (t) cc_final: 0.8313 (m) REVERT: C 154 SER cc_start: 0.9167 (t) cc_final: 0.8933 (p) REVERT: C 178 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9018 (ptm) REVERT: D 19 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7403 (ttt180) REVERT: D 178 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8952 (ptm) REVERT: E 154 SER cc_start: 0.9165 (t) cc_final: 0.8908 (p) REVERT: E 178 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8784 (ptm) REVERT: F 154 SER cc_start: 0.9156 (t) cc_final: 0.8897 (p) REVERT: G 154 SER cc_start: 0.9129 (t) cc_final: 0.8872 (p) REVERT: G 178 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8776 (ptm) REVERT: H 178 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8796 (ptm) REVERT: I 154 SER cc_start: 0.9133 (t) cc_final: 0.8867 (p) REVERT: I 178 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8619 (ptm) REVERT: I 186 VAL cc_start: 0.8897 (t) cc_final: 0.8352 (m) REVERT: J 154 SER cc_start: 0.9129 (t) cc_final: 0.8869 (p) REVERT: J 178 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8652 (ptm) REVERT: K 19 ARG cc_start: 0.7817 (mtm180) cc_final: 0.7327 (ttt180) REVERT: K 154 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9065 (p) REVERT: K 178 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8776 (ptm) REVERT: L 19 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7307 (ttt180) REVERT: L 154 SER cc_start: 0.9131 (t) cc_final: 0.8866 (p) REVERT: L 178 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8659 (ptm) REVERT: M 154 SER cc_start: 0.9135 (t) cc_final: 0.8871 (p) REVERT: M 178 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8834 (ptm) REVERT: N 178 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8898 (ptm) REVERT: O 19 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7365 (ttt180) REVERT: O 154 SER cc_start: 0.9118 (t) cc_final: 0.8848 (p) REVERT: O 178 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8653 (ptm) REVERT: P 178 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8777 (ptm) REVERT: Q 19 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7388 (ttt180) REVERT: Q 154 SER cc_start: 0.9133 (t) cc_final: 0.8873 (p) REVERT: Q 178 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8707 (ptm) REVERT: Q 186 VAL cc_start: 0.8934 (t) cc_final: 0.8375 (m) REVERT: R 154 SER cc_start: 0.9139 (t) cc_final: 0.8865 (p) REVERT: R 178 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8654 (ptm) REVERT: S 19 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7407 (ttt180) REVERT: S 178 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8905 (ptm) REVERT: T 178 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8695 (ptm) REVERT: U 178 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: U 186 VAL cc_start: 0.8922 (t) cc_final: 0.8344 (m) REVERT: V 19 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7406 (ttt180) REVERT: V 178 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8927 (ptm) REVERT: W 178 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8839 (ptm) REVERT: X 154 SER cc_start: 0.9154 (t) cc_final: 0.8885 (p) outliers start: 168 outliers final: 144 residues processed: 770 average time/residue: 0.2850 time to fit residues: 349.0619 Evaluate side-chains 762 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 596 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 178 MET Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 178 MET Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 178 MET Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 130 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 178 MET Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 130 SER Chi-restraints excluded: chain P residue 141 LEU Chi-restraints excluded: chain P residue 178 MET Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 130 SER Chi-restraints excluded: chain Q residue 141 LEU Chi-restraints excluded: chain Q residue 178 MET Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 178 MET Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 110 VAL Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 141 LEU Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain T residue 111 VAL Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 130 SER Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 130 SER Chi-restraints excluded: chain U residue 141 LEU Chi-restraints excluded: chain U residue 178 MET Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 111 VAL Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 130 SER Chi-restraints excluded: chain V residue 141 LEU Chi-restraints excluded: chain V residue 178 MET Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 40 ASN Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain W residue 141 LEU Chi-restraints excluded: chain W residue 178 MET Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain X residue 130 SER Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 3 optimal weight: 2.9990 chunk 525 optimal weight: 0.9980 chunk 383 optimal weight: 4.9990 chunk 546 optimal weight: 3.9990 chunk 376 optimal weight: 0.6980 chunk 352 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 391 optimal weight: 20.0000 chunk 450 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN D 40 ASN E 40 ASN K 40 ASN L 77 GLN M 40 ASN Q 40 ASN T 40 ASN V 40 ASN W 40 ASN X 40 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096482 restraints weight = 59237.038| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.62 r_work: 0.2923 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44808 Z= 0.125 Angle : 0.532 6.513 60432 Z= 0.276 Chirality : 0.045 0.162 6984 Planarity : 0.004 0.042 7872 Dihedral : 4.096 12.427 6168 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.75 % Allowed : 15.89 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.11), residues: 5568 helix: 2.25 (0.11), residues: 2040 sheet: -0.17 (0.12), residues: 1560 loop : -0.97 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 219 TYR 0.007 0.001 TYR V 199 PHE 0.011 0.001 PHE T 66 HIS 0.002 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00304 (44808) covalent geometry : angle 0.53176 (60432) hydrogen bonds : bond 0.03165 ( 2037) hydrogen bonds : angle 4.19652 ( 5679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9776.39 seconds wall clock time: 168 minutes 12.08 seconds (10092.08 seconds total)