Starting phenix.real_space_refine on Thu Dec 26 07:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_37965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_37965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_37965.map" model { file = "/net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_37965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x02_37965/12_2024/8x02_37965.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 8.86, per 1000 atoms: 0.20 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: 10.30 Conformation dependent library (CDL) restraints added in 5.9 seconds 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: 5.20 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: 16.97 Time building geometry restraints manager: 12.06 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: 0.00 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.550 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 76.490 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.200 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.820 ------------------------------------------------------------------------------- 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= 0.438 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (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 HIS 0.005 0.002 HIS J 48 PHE 0.022 0.003 PHE F 163 TYR 0.015 0.003 TYR N 204 ARG 0.006 0.001 ARG X 184 *********************** 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 : 5.390 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: 0.6783 time to fit residues: 1195.5986 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 : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 5.9990 chunk 418 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 322 optimal weight: 20.0000 chunk 501 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2634 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= 0.182 Angle : 0.581 5.265 60432 Z= 0.321 Chirality : 0.046 0.140 6984 Planarity : 0.006 0.052 7872 Dihedral : 4.963 16.897 6168 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.29 % Allowed : 9.45 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 5568 helix: -2.02 (0.09), residues: 2040 sheet: -1.27 (0.13), residues: 1272 loop : -1.39 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 206 PHE 0.010 0.001 PHE D 163 TYR 0.009 0.001 TYR J 199 ARG 0.005 0.001 ARG U 6 *********************** 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 931 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 822 time to evaluate : 5.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7507 (mtp85) REVERT: A 198 MET cc_start: 0.9184 (ttm) cc_final: 0.8879 (ttm) REVERT: B 19 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7504 (mtp85) REVERT: B 198 MET cc_start: 0.9192 (ttm) cc_final: 0.8898 (ttm) REVERT: C 19 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7512 (mtp85) REVERT: D 19 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7737 (ttt90) REVERT: E 19 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7459 (mtp85) REVERT: E 198 MET cc_start: 0.9177 (ttm) cc_final: 0.8954 (ttm) REVERT: F 19 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7470 (mtp85) REVERT: F 198 MET cc_start: 0.9183 (ttm) cc_final: 0.8882 (ttm) REVERT: G 19 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7563 (mtp85) REVERT: H 19 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7519 (mtp85) REVERT: H 198 MET cc_start: 0.9171 (ttm) cc_final: 0.8883 (ttm) REVERT: I 19 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7713 (ttt90) REVERT: I 186 VAL cc_start: 0.8734 (t) cc_final: 0.8189 (m) REVERT: I 198 MET cc_start: 0.9185 (ttm) cc_final: 0.8873 (ttm) REVERT: J 19 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7505 (mtp85) REVERT: K 19 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7732 (ttt90) REVERT: L 198 MET cc_start: 0.9192 (ttm) cc_final: 0.8907 (ttm) REVERT: M 19 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7517 (mtp85) REVERT: O 19 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7442 (mtp85) REVERT: O 198 MET cc_start: 0.9194 (ttm) cc_final: 0.8903 (ttm) REVERT: P 19 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7344 (mtp85) REVERT: P 198 MET cc_start: 0.9165 (ttm) cc_final: 0.8940 (ttm) REVERT: Q 19 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7475 (mtp85) REVERT: Q 198 MET cc_start: 0.9177 (ttm) cc_final: 0.8861 (ttm) REVERT: R 19 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7516 (mtp85) REVERT: R 198 MET cc_start: 0.9185 (ttm) cc_final: 0.8885 (ttm) REVERT: S 19 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7433 (mtp85) REVERT: T 19 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7498 (mtp85) REVERT: T 198 MET cc_start: 0.9182 (ttm) cc_final: 0.8908 (ttm) REVERT: U 19 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7515 (mtp85) REVERT: U 198 MET cc_start: 0.9187 (ttm) cc_final: 0.8882 (ttm) REVERT: V 19 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7753 (ttt90) REVERT: W 19 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7496 (mtp85) REVERT: W 198 MET cc_start: 0.9182 (ttm) cc_final: 0.8913 (ttm) REVERT: X 19 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7519 (mtp85) REVERT: X 198 MET cc_start: 0.9184 (ttm) cc_final: 0.8886 (ttm) outliers start: 109 outliers final: 84 residues processed: 916 average time/residue: 0.6601 time to fit residues: 942.4457 Evaluate side-chains 695 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 611 time to evaluate : 5.488 ------------------------------------------------------------------------------- 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 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 278 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 341 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 502 optimal weight: 2.9990 chunk 542 optimal weight: 3.9990 chunk 447 optimal weight: 3.9990 chunk 497 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 77 GLN B 42 GLN B 77 GLN E 42 GLN G 42 GLN I 42 GLN I 77 GLN J 42 GLN L 42 GLN ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN O 42 GLN Q 42 GLN Q 77 GLN R 77 GLN U 42 GLN X 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 44808 Z= 0.288 Angle : 0.602 7.265 60432 Z= 0.316 Chirality : 0.046 0.130 6984 Planarity : 0.005 0.040 7872 Dihedral : 4.807 17.730 6168 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.87 % Allowed : 10.54 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.10), residues: 5568 helix: -0.48 (0.10), residues: 2064 sheet: -0.97 (0.13), residues: 1296 loop : -1.38 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 179 PHE 0.024 0.002 PHE M 66 TYR 0.012 0.002 TYR G 199 ARG 0.005 0.000 ARG V 11 *********************** 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 799 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 615 time to evaluate : 5.210 Fit side-chains REVERT: A 19 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7402 (mtp85) REVERT: B 19 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7338 (mtp85) REVERT: C 19 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7334 (mtp180) REVERT: D 19 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7707 (ttt180) REVERT: D 186 VAL cc_start: 0.8801 (t) cc_final: 0.8345 (m) REVERT: E 19 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7333 (mtp85) REVERT: F 19 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7336 (mtp85) REVERT: G 19 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7727 (ttt180) REVERT: G 198 MET cc_start: 0.9183 (ttm) cc_final: 0.8982 (ttm) REVERT: H 19 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7345 (mtp85) REVERT: I 186 VAL cc_start: 0.8800 (t) cc_final: 0.8393 (m) REVERT: I 198 MET cc_start: 0.9230 (ttm) cc_final: 0.8918 (ttm) REVERT: J 19 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7409 (mtp85) REVERT: K 19 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7313 (mtp85) REVERT: M 19 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7723 (ttt180) REVERT: O 19 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7312 (mtp85) REVERT: P 19 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7337 (mtp85) REVERT: P 26 THR cc_start: 0.9049 (m) cc_final: 0.8835 (m) REVERT: Q 19 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7382 (mtp85) REVERT: R 19 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7398 (mtp85) REVERT: S 19 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7336 (mtp85) REVERT: S 186 VAL cc_start: 0.8795 (t) cc_final: 0.8334 (m) REVERT: T 19 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7335 (mtp85) REVERT: U 19 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7408 (mtp85) REVERT: V 19 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7722 (ttt180) REVERT: V 186 VAL cc_start: 0.8793 (t) cc_final: 0.8344 (m) REVERT: W 19 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7396 (mtp85) REVERT: X 19 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7343 (mtp85) outliers start: 184 outliers final: 157 residues processed: 752 average time/residue: 0.6664 time to fit residues: 812.3843 Evaluate side-chains 704 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 547 time to evaluate : 5.519 ------------------------------------------------------------------------------- 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 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 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 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 16 ILE 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 76 GLU 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 16 ILE 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 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 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 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 76 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 7.9990 chunk 377 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 503 optimal weight: 3.9990 chunk 533 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 chunk 477 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 206 HIS B 77 GLN B 206 HIS C 42 GLN C 206 HIS D 42 GLN D 206 HIS E 206 HIS F 42 GLN F 77 GLN F 206 HIS G 206 HIS H 42 GLN H 206 HIS I 77 GLN I 206 HIS J 77 GLN J 206 HIS K 42 GLN K 206 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN M 206 HIS N 206 HIS O 206 HIS P 42 GLN P 206 HIS ** Q 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 GLN R 77 GLN R 206 HIS S 42 GLN S 77 GLN S 206 HIS T 42 GLN T 206 HIS U 206 HIS V 42 GLN V 206 HIS W 42 GLN W 206 HIS X 42 GLN X 206 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 44808 Z= 0.387 Angle : 0.630 6.546 60432 Z= 0.332 Chirality : 0.048 0.161 6984 Planarity : 0.005 0.039 7872 Dihedral : 5.020 20.240 6168 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.31 % Allowed : 12.35 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.10), residues: 5568 helix: -0.10 (0.10), residues: 2064 sheet: -0.75 (0.13), residues: 1296 loop : -1.35 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS W 56 PHE 0.025 0.002 PHE P 66 TYR 0.015 0.002 TYR U 199 ARG 0.004 0.000 ARG V 11 *********************** 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 789 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 584 time to evaluate : 5.276 Fit side-chains REVERT: A 40 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 7 GLU cc_start: 0.7567 (tp30) cc_final: 0.7275 (tp30) REVERT: B 18 GLN cc_start: 0.9070 (tp40) cc_final: 0.8601 (tp-100) REVERT: B 40 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8346 (t0) REVERT: C 18 GLN cc_start: 0.9089 (tp40) cc_final: 0.8619 (tp-100) REVERT: C 40 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8246 (t0) REVERT: D 186 VAL cc_start: 0.8825 (t) cc_final: 0.8459 (m) REVERT: E 40 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (t0) REVERT: F 40 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8258 (t0) REVERT: G 40 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8236 (t0) REVERT: H 18 GLN cc_start: 0.9088 (tp40) cc_final: 0.8619 (tp-100) REVERT: H 40 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8231 (t0) REVERT: I 7 GLU cc_start: 0.7534 (tp30) cc_final: 0.7235 (tp30) REVERT: I 186 VAL cc_start: 0.8818 (t) cc_final: 0.8482 (m) REVERT: I 198 MET cc_start: 0.9198 (ttm) cc_final: 0.8947 (ttm) REVERT: J 40 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8260 (t0) REVERT: K 40 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (t0) REVERT: L 40 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8266 (t0) REVERT: N 40 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8254 (t0) REVERT: O 7 GLU cc_start: 0.7602 (tp30) cc_final: 0.7282 (tp30) REVERT: O 40 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8259 (t0) REVERT: P 7 GLU cc_start: 0.7525 (tp30) cc_final: 0.7216 (tp30) REVERT: P 40 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (t0) REVERT: Q 18 GLN cc_start: 0.9106 (tp40) cc_final: 0.8643 (tp-100) REVERT: Q 40 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8288 (t0) REVERT: R 40 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8260 (t0) REVERT: S 7 GLU cc_start: 0.7548 (tp30) cc_final: 0.7242 (tp30) REVERT: S 40 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (t0) REVERT: S 186 VAL cc_start: 0.8833 (t) cc_final: 0.8468 (m) REVERT: T 7 GLU cc_start: 0.7544 (tp30) cc_final: 0.7247 (tp30) REVERT: T 40 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (t0) REVERT: U 40 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8251 (t0) REVERT: V 40 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8241 (t0) REVERT: V 186 VAL cc_start: 0.8833 (t) cc_final: 0.8476 (m) outliers start: 205 outliers final: 179 residues processed: 765 average time/residue: 0.6550 time to fit residues: 787.3625 Evaluate side-chains 759 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 561 time to evaluate : 5.309 ------------------------------------------------------------------------------- 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 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 16 ILE 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 C residue 186 VAL 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 E residue 186 VAL Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 16 ILE 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 F residue 186 VAL Chi-restraints excluded: chain G residue 1 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 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 16 ILE 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 H residue 186 VAL 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 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 K residue 186 VAL 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 16 ILE 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 M residue 186 VAL Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 16 ILE 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 154 SER 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 O residue 186 VAL Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 16 ILE 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 P residue 186 VAL Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 16 ILE 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 16 ILE 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 R residue 186 VAL Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 16 ILE 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 154 SER 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 T residue 186 VAL Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 16 ILE 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 16 ILE 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 Chi-restraints excluded: chain X residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 397 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 455 optimal weight: 2.9990 chunk 368 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 478 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 ASN ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 44808 Z= 0.261 Angle : 0.553 6.576 60432 Z= 0.290 Chirality : 0.046 0.149 6984 Planarity : 0.004 0.040 7872 Dihedral : 4.623 16.680 6168 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.25 % Allowed : 12.79 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.11), residues: 5568 helix: 0.44 (0.11), residues: 2064 sheet: -0.52 (0.12), residues: 1560 loop : -1.39 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 56 PHE 0.014 0.002 PHE N 66 TYR 0.009 0.001 TYR U 199 ARG 0.004 0.000 ARG V 11 *********************** 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 782 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 580 time to evaluate : 6.110 Fit side-chains REVERT: B 7 GLU cc_start: 0.7597 (tp30) cc_final: 0.7273 (tp30) REVERT: B 40 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8213 (t0) REVERT: D 154 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9048 (p) REVERT: D 186 VAL cc_start: 0.8816 (t) cc_final: 0.8391 (m) REVERT: I 7 GLU cc_start: 0.7621 (tp30) cc_final: 0.7298 (tp30) REVERT: I 186 VAL cc_start: 0.8856 (t) cc_final: 0.8426 (m) REVERT: K 154 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9051 (p) REVERT: Q 18 GLN cc_start: 0.9104 (tp40) cc_final: 0.8669 (tp-100) REVERT: S 186 VAL cc_start: 0.8827 (t) cc_final: 0.8408 (m) REVERT: T 7 GLU cc_start: 0.7606 (tp30) cc_final: 0.7294 (tp30) REVERT: V 7 GLU cc_start: 0.7662 (tp30) cc_final: 0.7349 (tp30) REVERT: V 186 VAL cc_start: 0.8814 (t) cc_final: 0.8392 (m) REVERT: X 18 GLN cc_start: 0.9104 (tp40) cc_final: 0.8675 (tp-100) outliers start: 202 outliers final: 174 residues processed: 757 average time/residue: 0.6675 time to fit residues: 811.0238 Evaluate side-chains 732 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 555 time to evaluate : 5.004 ------------------------------------------------------------------------------- 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 A residue 186 VAL 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 B residue 186 VAL 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 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 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 G residue 186 VAL 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 J residue 186 VAL 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 154 SER 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 L residue 186 VAL 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 N residue 186 VAL 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 85 ASP 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 Q residue 186 VAL 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 U residue 186 VAL 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 W residue 186 VAL 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 179 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 C 40 ASN D 40 ASN E 40 ASN F 40 ASN H 40 ASN I 40 ASN J 40 ASN K 40 ASN L 40 ASN L 206 HIS M 40 ASN N 40 ASN O 40 ASN P 40 ASN Q 40 ASN Q 206 HIS R 40 ASN S 40 ASN T 40 ASN U 40 ASN V 40 ASN W 40 ASN X 40 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 44808 Z= 0.386 Angle : 0.619 6.605 60432 Z= 0.325 Chirality : 0.048 0.167 6984 Planarity : 0.004 0.040 7872 Dihedral : 4.901 19.068 6168 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.56 % Allowed : 12.77 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.10), residues: 5568 helix: 0.39 (0.11), residues: 2064 sheet: -0.76 (0.11), residues: 1560 loop : -1.44 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 206 PHE 0.021 0.002 PHE H 66 TYR 0.013 0.002 TYR J 199 ARG 0.003 0.000 ARG V 11 *********************** 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 860 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 596 time to evaluate : 5.439 Fit side-chains REVERT: B 7 GLU cc_start: 0.7586 (tp30) cc_final: 0.7249 (tp30) REVERT: B 18 GLN cc_start: 0.9076 (tp40) cc_final: 0.8612 (tp-100) REVERT: C 18 GLN cc_start: 0.9072 (tp40) cc_final: 0.8597 (tp-100) REVERT: D 186 VAL cc_start: 0.8845 (t) cc_final: 0.8452 (m) REVERT: E 18 GLN cc_start: 0.9091 (tp40) cc_final: 0.8642 (tp-100) REVERT: H 18 GLN cc_start: 0.9077 (tp40) cc_final: 0.8608 (tp-100) REVERT: I 7 GLU cc_start: 0.7633 (tp30) cc_final: 0.7300 (tp30) REVERT: I 186 VAL cc_start: 0.8879 (t) cc_final: 0.8485 (m) REVERT: J 18 GLN cc_start: 0.9037 (tp40) cc_final: 0.8640 (tp-100) REVERT: M 18 GLN cc_start: 0.9073 (tp40) cc_final: 0.8602 (tp-100) REVERT: Q 18 GLN cc_start: 0.9100 (tp40) cc_final: 0.8638 (tp-100) REVERT: S 186 VAL cc_start: 0.8842 (t) cc_final: 0.8432 (m) REVERT: U 18 GLN cc_start: 0.9037 (tp40) cc_final: 0.8639 (tp-100) REVERT: V 7 GLU cc_start: 0.7615 (tp30) cc_final: 0.7285 (tp30) REVERT: V 186 VAL cc_start: 0.8835 (t) cc_final: 0.8473 (m) REVERT: X 18 GLN cc_start: 0.9096 (tp40) cc_final: 0.8639 (tp-100) outliers start: 264 outliers final: 237 residues processed: 826 average time/residue: 0.6002 time to fit residues: 800.4636 Evaluate side-chains 827 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 590 time to evaluate : 5.404 ------------------------------------------------------------------------------- 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 110 VAL 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 A residue 186 VAL Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 110 VAL 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 B residue 186 VAL Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 110 VAL 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 C residue 186 VAL Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 40 ASN 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 154 SER 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 E residue 186 VAL Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 110 VAL 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 F residue 186 VAL Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 110 VAL 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 G residue 186 VAL Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 110 VAL 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 H residue 186 VAL Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 110 VAL 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 40 ASN Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 110 VAL 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 J residue 186 VAL Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 85 ASP 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 K residue 186 VAL 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 L residue 186 VAL Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 110 VAL 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 M residue 186 VAL Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 40 ASN Chi-restraints excluded: chain N residue 110 VAL 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 154 SER Chi-restraints excluded: chain N residue 178 MET Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 40 ASN Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 110 VAL 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 O residue 186 VAL Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 110 VAL 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 P residue 186 VAL Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 110 VAL 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 Q residue 186 VAL Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 110 VAL 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 R residue 186 VAL Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 16 ILE Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 85 ASP 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 16 ILE Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 110 VAL 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 T residue 186 VAL Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 110 VAL 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 U residue 186 VAL Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 110 VAL 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 40 ASN Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 110 VAL 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 W residue 186 VAL Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 40 ASN Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 110 VAL 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 Chi-restraints excluded: chain X residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 390 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 532 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 5 HIS I 40 ASN P 5 HIS S 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3801 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= 0.200 Angle : 0.549 6.671 60432 Z= 0.285 Chirality : 0.045 0.159 6984 Planarity : 0.004 0.040 7872 Dihedral : 4.482 15.834 6168 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.38 % Allowed : 13.40 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 5568 helix: 0.99 (0.11), residues: 2040 sheet: -0.59 (0.12), residues: 1560 loop : -1.19 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS S 5 PHE 0.010 0.001 PHE G 66 TYR 0.007 0.001 TYR K 199 ARG 0.003 0.000 ARG V 11 *********************** 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 796 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 588 time to evaluate : 5.343 Fit side-chains REVERT: B 178 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8657 (ptm) REVERT: C 178 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8621 (ptm) REVERT: D 154 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.9038 (p) REVERT: D 178 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8609 (ptm) REVERT: D 186 VAL cc_start: 0.8821 (t) cc_final: 0.8387 (m) REVERT: E 18 GLN cc_start: 0.9114 (tp40) cc_final: 0.8690 (tp-100) REVERT: E 178 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8583 (ptm) REVERT: G 178 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8586 (ptm) REVERT: H 178 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8569 (ptm) REVERT: I 186 VAL cc_start: 0.8860 (t) cc_final: 0.8398 (m) REVERT: J 178 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8751 (ptm) REVERT: K 154 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (p) REVERT: K 178 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8578 (ptm) REVERT: M 178 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8592 (ptm) REVERT: N 178 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8608 (ptm) REVERT: P 178 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8581 (ptm) REVERT: Q 18 GLN cc_start: 0.9096 (tp40) cc_final: 0.8672 (tp-100) REVERT: S 154 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.9038 (p) REVERT: S 178 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8604 (ptm) REVERT: S 186 VAL cc_start: 0.8858 (t) cc_final: 0.8408 (m) REVERT: T 178 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8754 (ptm) REVERT: U 178 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: V 154 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.9039 (p) REVERT: V 178 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8631 (ptm) REVERT: V 186 VAL cc_start: 0.8833 (t) cc_final: 0.8395 (m) REVERT: W 178 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8598 (ptm) REVERT: X 18 GLN cc_start: 0.9095 (tp40) cc_final: 0.8677 (tp-100) REVERT: X 178 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (ptm) outliers start: 208 outliers final: 174 residues processed: 770 average time/residue: 0.6073 time to fit residues: 747.8567 Evaluate side-chains 763 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 568 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 110 VAL 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 A residue 186 VAL Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 110 VAL 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 110 VAL 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 154 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 1 LEU 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 E residue 186 VAL Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 110 VAL 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 F residue 186 VAL Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 110 VAL 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 110 VAL 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 H residue 186 VAL Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 110 VAL 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 85 ASP 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 J residue 186 VAL 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 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 L residue 186 VAL Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 110 VAL 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 110 VAL 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 N residue 186 VAL Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 85 ASP Chi-restraints excluded: chain O residue 110 VAL 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 85 ASP Chi-restraints excluded: chain P residue 110 VAL 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 P residue 186 VAL Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 85 ASP 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 Q residue 186 VAL Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 85 ASP 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 R residue 186 VAL Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 85 ASP 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 154 SER Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 110 VAL 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 T residue 186 VAL Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 110 VAL 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 110 VAL 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 85 ASP Chi-restraints excluded: chain W residue 110 VAL 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 W residue 186 VAL Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 110 VAL 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 Chi-restraints excluded: chain X residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 10.0000 chunk 212 optimal weight: 0.0020 chunk 317 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 362 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 418 optimal weight: 6.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 44808 Z= 0.140 Angle : 0.508 6.691 60432 Z= 0.263 Chirality : 0.044 0.167 6984 Planarity : 0.004 0.041 7872 Dihedral : 3.983 11.224 6168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.61 % Allowed : 15.70 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5568 helix: 1.88 (0.11), residues: 2040 sheet: -0.32 (0.12), residues: 1560 loop : -0.93 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 5 PHE 0.010 0.001 PHE G 217 TYR 0.004 0.001 TYR P 122 ARG 0.003 0.000 ARG V 11 *********************** 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 838 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 714 time to evaluate : 5.155 Fit side-chains REVERT: A 178 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8041 (ptm) REVERT: B 7 GLU cc_start: 0.7351 (mp0) cc_final: 0.6853 (mt-10) REVERT: B 154 SER cc_start: 0.9180 (t) cc_final: 0.8965 (p) REVERT: B 178 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8031 (ptm) REVERT: C 178 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8065 (ptm) REVERT: D 178 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8028 (ptm) REVERT: E 178 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8062 (ptm) REVERT: F 178 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8098 (ptm) REVERT: G 75 GLN cc_start: 0.8774 (tt0) cc_final: 0.8557 (tt0) REVERT: G 178 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8064 (ptm) REVERT: H 178 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8050 (ptm) REVERT: I 7 GLU cc_start: 0.7342 (mp0) cc_final: 0.6851 (mt-10) REVERT: I 178 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8102 (ptm) REVERT: I 186 VAL cc_start: 0.8834 (t) cc_final: 0.8327 (m) REVERT: J 178 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8053 (ptm) REVERT: K 178 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8053 (ptm) REVERT: L 154 SER cc_start: 0.9203 (t) cc_final: 0.8999 (p) REVERT: L 178 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8042 (ptm) REVERT: M 75 GLN cc_start: 0.8772 (tt0) cc_final: 0.8544 (tt0) REVERT: M 178 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8072 (ptm) REVERT: N 75 GLN cc_start: 0.8771 (tt0) cc_final: 0.8552 (tt0) REVERT: N 178 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8024 (ptm) REVERT: O 178 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8081 (ptm) REVERT: P 26 THR cc_start: 0.8861 (m) cc_final: 0.8647 (m) REVERT: P 75 GLN cc_start: 0.8766 (tt0) cc_final: 0.8548 (tt0) REVERT: P 178 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8058 (ptm) REVERT: Q 178 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8029 (ptm) REVERT: R 154 SER cc_start: 0.9182 (t) cc_final: 0.8963 (p) REVERT: R 178 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8026 (ptm) REVERT: S 178 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8030 (ptm) REVERT: T 154 SER cc_start: 0.9166 (t) cc_final: 0.8965 (p) REVERT: T 178 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: U 154 SER cc_start: 0.9166 (t) cc_final: 0.8958 (p) REVERT: U 178 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8103 (ptm) REVERT: V 178 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8022 (ptm) REVERT: W 75 GLN cc_start: 0.8774 (tt0) cc_final: 0.8549 (tt0) REVERT: W 178 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8065 (ptm) REVERT: X 154 SER cc_start: 0.9203 (t) cc_final: 0.8996 (p) REVERT: X 178 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8083 (ptm) outliers start: 124 outliers final: 99 residues processed: 814 average time/residue: 0.5951 time to fit residues: 779.0495 Evaluate side-chains 708 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 585 time to evaluate : 5.199 ------------------------------------------------------------------------------- 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 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 110 VAL 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 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 1 LEU 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 110 VAL 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 110 VAL 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 465 optimal weight: 0.0770 chunk 495 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 389 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 448 optimal weight: 0.9990 chunk 468 optimal weight: 0.8980 chunk 494 optimal weight: 7.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 5 HIS D 25 ASN E 40 ASN I 5 HIS L 40 ASN R 77 GLN S 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 44808 Z= 0.160 Angle : 0.523 10.250 60432 Z= 0.269 Chirality : 0.045 0.150 6984 Planarity : 0.004 0.042 7872 Dihedral : 3.967 10.624 6168 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.78 % Allowed : 16.77 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.11), residues: 5568 helix: 2.16 (0.11), residues: 2040 sheet: -0.20 (0.12), residues: 1560 loop : -0.94 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 5 PHE 0.008 0.001 PHE U 217 TYR 0.006 0.001 TYR D 199 ARG 0.004 0.000 ARG S 11 *********************** 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 758 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 626 time to evaluate : 5.592 Fit side-chains REVERT: A 178 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8368 (ptm) REVERT: B 7 GLU cc_start: 0.7157 (mp0) cc_final: 0.6873 (mt-10) REVERT: B 154 SER cc_start: 0.9111 (t) cc_final: 0.8909 (p) REVERT: B 178 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8401 (ptm) REVERT: C 178 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8247 (ptm) REVERT: D 178 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8280 (ptm) REVERT: E 178 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8192 (ptm) REVERT: F 178 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8320 (ptm) REVERT: G 75 GLN cc_start: 0.8799 (tt0) cc_final: 0.8566 (tt0) REVERT: G 126 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7838 (mm-30) REVERT: G 178 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8193 (ptm) REVERT: H 178 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8223 (ptm) REVERT: I 7 GLU cc_start: 0.7202 (mp0) cc_final: 0.6933 (mt-10) REVERT: I 178 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8285 (ptm) REVERT: I 186 VAL cc_start: 0.8816 (t) cc_final: 0.8304 (m) REVERT: J 178 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8422 (ptm) REVERT: K 178 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8226 (ptm) REVERT: L 178 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8419 (ptm) REVERT: M 75 GLN cc_start: 0.8784 (tt0) cc_final: 0.8561 (tt0) REVERT: M 178 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8245 (ptm) REVERT: N 75 GLN cc_start: 0.8792 (tt0) cc_final: 0.8570 (tt0) REVERT: N 178 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8282 (ptm) REVERT: O 178 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8432 (ptm) REVERT: P 26 THR cc_start: 0.8857 (m) cc_final: 0.8656 (m) REVERT: P 75 GLN cc_start: 0.8806 (tt0) cc_final: 0.8581 (tt0) REVERT: P 178 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8262 (ptm) REVERT: Q 178 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8383 (ptm) REVERT: R 154 SER cc_start: 0.9110 (t) cc_final: 0.8906 (p) REVERT: R 178 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8401 (ptm) REVERT: S 178 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8273 (ptm) REVERT: T 178 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8404 (ptm) REVERT: U 178 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8419 (ptm) REVERT: V 178 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8293 (ptm) REVERT: W 75 GLN cc_start: 0.8786 (tt0) cc_final: 0.8563 (tt0) REVERT: W 178 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8266 (ptm) REVERT: X 178 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8406 (ptm) outliers start: 132 outliers final: 102 residues processed: 733 average time/residue: 0.6259 time to fit residues: 731.6182 Evaluate side-chains 718 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 592 time to evaluate : 5.443 ------------------------------------------------------------------------------- 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 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 40 ASN 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 110 VAL 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 40 ASN 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 1 LEU Chi-restraints excluded: chain P residue 76 GLU 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 110 VAL 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 110 VAL 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 4.9990 chunk 524 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 549 optimal weight: 2.9990 chunk 506 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 chunk 45 optimal weight: 0.0000 chunk 338 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 77 GLN E 40 ASN G 40 ASN I 77 GLN J 77 GLN L 40 ASN O 40 ASN P 40 ASN Q 40 ASN R 77 GLN S 40 ASN S 77 GLN V 40 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 44808 Z= 0.247 Angle : 0.560 6.465 60432 Z= 0.290 Chirality : 0.046 0.168 6984 Planarity : 0.004 0.043 7872 Dihedral : 4.188 11.046 6168 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.97 % Allowed : 16.75 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 5568 helix: 2.05 (0.11), residues: 2064 sheet: -0.21 (0.12), residues: 1560 loop : -1.13 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS V 48 PHE 0.013 0.002 PHE L 66 TYR 0.008 0.001 TYR S 199 ARG 0.003 0.000 ARG V 11 ********************** 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 723 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 582 time to evaluate : 5.212 Fit side-chains REVERT: I 186 VAL cc_start: 0.8863 (t) cc_final: 0.8423 (m) outliers start: 141 outliers final: 136 residues processed: 697 average time/residue: 0.6351 time to fit residues: 701.4982 Evaluate side-chains 711 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 575 time to evaluate : 5.210 ------------------------------------------------------------------------------- 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 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 85 ASP 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 40 ASN 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 40 ASN 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 85 ASP 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 85 ASP 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 110 VAL 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 40 ASN Chi-restraints excluded: chain L residue 85 ASP 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 40 ASN 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 1 LEU Chi-restraints excluded: chain P residue 40 ASN 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 40 ASN Chi-restraints excluded: chain Q residue 110 VAL 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 85 ASP Chi-restraints excluded: chain R residue 110 VAL 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 40 ASN 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 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 40 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 6.9990 chunk 466 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 438 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 450 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 77 GLN B 77 GLN C 40 ASN G 40 ASN I 77 GLN J 77 GLN O 40 ASN P 40 ASN Q 40 ASN R 77 GLN S 40 ASN S 77 GLN T 40 ASN V 40 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092394 restraints weight = 59109.267| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.58 r_work: 0.2892 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 44808 Z= 0.297 Angle : 0.578 6.438 60432 Z= 0.299 Chirality : 0.046 0.165 6984 Planarity : 0.004 0.043 7872 Dihedral : 4.252 11.947 6168 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.18 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5568 helix: 2.03 (0.11), residues: 2064 sheet: -0.21 (0.12), residues: 1560 loop : -1.23 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 48 PHE 0.014 0.002 PHE B 66 TYR 0.009 0.001 TYR S 199 ARG 0.003 0.000 ARG V 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12661.42 seconds wall clock time: 231 minutes 5.25 seconds (13865.25 seconds total)