Starting phenix.real_space_refine on Fri Sep 27 05:25:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/09_2024/5tfy_8405.cif" } resolution = 3.4 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 20852 2.51 5 N 5096 2.21 5 O 6110 1.98 5 H 33046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65182 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} 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, Y, X, Z Time building chain proxies: 11.22, per 1000 atoms: 0.17 Number of scatterers: 65182 At special positions: 0 Unit cell: (102.7, 105.3, 245.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 O 6110 8.00 N 5096 7.00 C 20852 6.00 H 33046 1.00 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: 13.08 Conformation dependent library (CDL) restraints added in 3.9 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7592 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 78 sheets defined 30.4% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'I' and resid 2 through 48 removed outlier: 3.937A pdb=" N ALA I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 12 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'A' and resid 2 through 48 removed outlier: 3.939A pdb=" N ALA A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'B' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'C' and resid 2 through 48 removed outlier: 3.940A pdb=" N ALA C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'D' and resid 2 through 48 removed outlier: 3.937A pdb=" N ALA D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'E' and resid 2 through 48 removed outlier: 3.934A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 12 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'F' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'H' and resid 2 through 48 removed outlier: 3.931A pdb=" N ALA H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 12 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'J' and resid 2 through 48 removed outlier: 3.936A pdb=" N ALA J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'K' and resid 2 through 48 removed outlier: 3.938A pdb=" N ALA K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 12 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'L' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'M' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA M 6 " --> pdb=" O SER M 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA M 12 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA M 46 " --> pdb=" O GLY M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'N' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA N 6 " --> pdb=" O SER N 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'O' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 88 No H-bonds generated for 'chain 'O' and resid 86 through 88' Processing helix chain 'P' and resid 2 through 48 removed outlier: 3.935A pdb=" N ALA P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 88 No H-bonds generated for 'chain 'P' and resid 86 through 88' Processing helix chain 'Q' and resid 2 through 48 removed outlier: 3.943A pdb=" N ALA Q 6 " --> pdb=" O SER Q 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA Q 46 " --> pdb=" O GLY Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'R' and resid 2 through 48 removed outlier: 3.943A pdb=" N ALA R 6 " --> pdb=" O SER R 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA R 12 " --> pdb=" O ILE R 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 46 " --> pdb=" O GLY R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA S 6 " --> pdb=" O SER S 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 46 " --> pdb=" O GLY S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 88 No H-bonds generated for 'chain 'S' and resid 86 through 88' Processing helix chain 'T' and resid 2 through 48 removed outlier: 3.932A pdb=" N ALA T 6 " --> pdb=" O SER T 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 88 No H-bonds generated for 'chain 'T' and resid 86 through 88' Processing helix chain 'U' and resid 2 through 48 removed outlier: 3.932A pdb=" N ALA U 6 " --> pdb=" O SER U 2 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'V' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA V 6 " --> pdb=" O SER V 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA V 12 " --> pdb=" O ILE V 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 88 No H-bonds generated for 'chain 'V' and resid 86 through 88' Processing helix chain 'W' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA W 12 " --> pdb=" O ILE W 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR W 39 " --> pdb=" O SER W 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA W 46 " --> pdb=" O GLY W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'X' and resid 2 through 48 removed outlier: 3.946A pdb=" N ALA X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA X 12 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR X 39 " --> pdb=" O SER X 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA X 46 " --> pdb=" O GLY X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 88 No H-bonds generated for 'chain 'X' and resid 86 through 88' Processing helix chain 'Y' and resid 2 through 48 removed outlier: 3.936A pdb=" N ALA Y 6 " --> pdb=" O SER Y 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Y 12 " --> pdb=" O ILE Y 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR Y 39 " --> pdb=" O SER Y 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Y 46 " --> pdb=" O GLY Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 88 No H-bonds generated for 'chain 'Y' and resid 86 through 88' Processing helix chain 'Z' and resid 2 through 48 removed outlier: 3.934A pdb=" N ALA Z 6 " --> pdb=" O SER Z 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA Z 12 " --> pdb=" O ILE Z 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR Z 39 " --> pdb=" O SER Z 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 46 " --> pdb=" O GLY Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 88 No H-bonds generated for 'chain 'Z' and resid 86 through 88' Processing sheet with id=AA1, first strand: chain 'I' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER I 104 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN I 69 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR I 73 " --> pdb=" O MET I 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 55 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS I 75 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP I 53 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 56 " --> pdb=" O ILE I 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84 Processing sheet with id=AA3, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 4.801A pdb=" N SER A 104 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 69 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR A 73 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET A 55 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 75 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 53 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 56 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER B 104 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 69 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 73 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET B 55 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 75 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 53 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 56 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 105 removed outlier: 4.790A pdb=" N SER C 104 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 69 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR C 73 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET C 55 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS C 75 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP C 53 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE C 56 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB4, first strand: chain 'D' and resid 104 through 105 removed outlier: 4.801A pdb=" N SER D 104 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN D 69 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR D 73 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET D 55 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS D 75 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP D 53 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE D 56 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AB7, first strand: chain 'E' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER E 104 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 69 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR E 73 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET E 55 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 75 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP E 53 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE E 56 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'F' and resid 104 through 105 removed outlier: 4.796A pdb=" N SER F 104 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN F 69 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR F 73 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET F 55 " --> pdb=" O TYR F 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS F 75 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP F 53 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 56 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AC4, first strand: chain 'G' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER G 104 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN G 69 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR G 73 " --> pdb=" O MET G 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET G 55 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS G 75 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP G 53 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE G 56 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC6, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AC7, first strand: chain 'H' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER H 104 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN H 69 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR H 73 " --> pdb=" O MET H 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET H 55 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS H 75 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP H 53 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE H 56 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 83 through 84 Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AD1, first strand: chain 'J' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER J 104 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR J 73 " --> pdb=" O MET J 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET J 55 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS J 75 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP J 53 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE J 56 " --> pdb=" O ILE J 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 83 through 84 Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'K' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER K 104 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN K 69 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR K 73 " --> pdb=" O MET K 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET K 55 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS K 75 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP K 53 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE K 56 " --> pdb=" O ILE K 163 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 83 through 84 Processing sheet with id=AD6, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AD7, first strand: chain 'L' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER L 104 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN L 69 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR L 73 " --> pdb=" O MET L 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET L 55 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS L 75 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP L 53 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE L 56 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AD9, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'M' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER M 104 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN M 69 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR M 73 " --> pdb=" O MET M 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET M 55 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS M 75 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP M 53 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE M 56 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 83 through 84 Processing sheet with id=AE3, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AE4, first strand: chain 'N' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER N 104 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN N 69 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR N 73 " --> pdb=" O MET N 55 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET N 55 " --> pdb=" O TYR N 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS N 75 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP N 53 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE N 56 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 83 through 84 Processing sheet with id=AE6, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AE7, first strand: chain 'O' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER O 104 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN O 69 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR O 73 " --> pdb=" O MET O 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET O 55 " --> pdb=" O TYR O 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS O 75 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP O 53 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE O 56 " --> pdb=" O ILE O 163 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 83 through 84 Processing sheet with id=AE9, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AF1, first strand: chain 'P' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER P 104 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN P 69 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR P 73 " --> pdb=" O MET P 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET P 55 " --> pdb=" O TYR P 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS P 75 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP P 53 " --> pdb=" O LYS P 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE P 56 " --> pdb=" O ILE P 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 83 through 84 Processing sheet with id=AF3, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=AF4, first strand: chain 'Q' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER Q 104 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN Q 69 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR Q 73 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET Q 55 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS Q 75 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP Q 53 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE Q 56 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 83 through 84 Processing sheet with id=AF6, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=AF7, first strand: chain 'R' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER R 104 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN R 69 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR R 73 " --> pdb=" O MET R 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET R 55 " --> pdb=" O TYR R 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS R 75 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP R 53 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE R 56 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 83 through 84 Processing sheet with id=AF9, first strand: chain 'R' and resid 100 through 101 Processing sheet with id=AG1, first strand: chain 'S' and resid 104 through 105 removed outlier: 4.790A pdb=" N SER S 104 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN S 69 " --> pdb=" O SER S 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR S 73 " --> pdb=" O MET S 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET S 55 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS S 75 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP S 53 " --> pdb=" O LYS S 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE S 56 " --> pdb=" O ILE S 163 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 83 through 84 Processing sheet with id=AG3, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=AG4, first strand: chain 'T' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER T 104 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN T 69 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR T 73 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET T 55 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS T 75 " --> pdb=" O ASP T 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP T 53 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE T 56 " --> pdb=" O ILE T 163 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 83 through 84 Processing sheet with id=AG6, first strand: chain 'T' and resid 100 through 101 Processing sheet with id=AG7, first strand: chain 'U' and resid 104 through 105 removed outlier: 4.796A pdb=" N SER U 104 " --> pdb=" O THR U 123 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN U 69 " --> pdb=" O SER U 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR U 73 " --> pdb=" O MET U 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET U 55 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS U 75 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP U 53 " --> pdb=" O LYS U 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE U 56 " --> pdb=" O ILE U 163 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 83 through 84 Processing sheet with id=AG9, first strand: chain 'U' and resid 100 through 101 Processing sheet with id=AH1, first strand: chain 'V' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER V 104 " --> pdb=" O THR V 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN V 69 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR V 73 " --> pdb=" O MET V 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET V 55 " --> pdb=" O TYR V 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS V 75 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP V 53 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE V 56 " --> pdb=" O ILE V 163 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 83 through 84 Processing sheet with id=AH3, first strand: chain 'V' and resid 100 through 101 Processing sheet with id=AH4, first strand: chain 'W' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER W 104 " --> pdb=" O THR W 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN W 69 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR W 73 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET W 55 " --> pdb=" O TYR W 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS W 75 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP W 53 " --> pdb=" O LYS W 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE W 56 " --> pdb=" O ILE W 163 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 83 through 84 Processing sheet with id=AH6, first strand: chain 'W' and resid 100 through 101 Processing sheet with id=AH7, first strand: chain 'X' and resid 104 through 105 removed outlier: 4.788A pdb=" N SER X 104 " --> pdb=" O THR X 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN X 69 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR X 73 " --> pdb=" O MET X 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET X 55 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS X 75 " --> pdb=" O ASP X 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP X 53 " --> pdb=" O LYS X 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE X 56 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 83 through 84 Processing sheet with id=AH9, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AI1, first strand: chain 'Y' and resid 104 through 105 removed outlier: 4.794A pdb=" N SER Y 104 " --> pdb=" O THR Y 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN Y 69 " --> pdb=" O SER Y 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR Y 73 " --> pdb=" O MET Y 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET Y 55 " --> pdb=" O TYR Y 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS Y 75 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP Y 53 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 163 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AI3, first strand: chain 'Y' and resid 100 through 101 Processing sheet with id=AI4, first strand: chain 'Z' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER Z 104 " --> pdb=" O THR Z 123 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Z 69 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR Z 73 " --> pdb=" O MET Z 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET Z 55 " --> pdb=" O TYR Z 73 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS Z 75 " --> pdb=" O ASP Z 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP Z 53 " --> pdb=" O LYS Z 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 163 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 83 through 84 Processing sheet with id=AI6, first strand: chain 'Z' and resid 100 through 101 1725 hydrogen bonds defined for protein. 4785 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: 27.33 Time building geometry restraints manager: 16.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 32968 1.02 - 1.22: 106 1.22 - 1.42: 13039 1.42 - 1.61: 19537 1.61 - 1.81: 156 Bond restraints: 65806 Sorted by residual: bond pdb=" N VAL I 99 " pdb=" H VAL I 99 " ideal model delta sigma weight residual 0.860 1.115 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N VAL Q 99 " pdb=" H VAL Q 99 " ideal model delta sigma weight residual 0.860 1.112 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" N VAL U 99 " pdb=" H VAL U 99 " ideal model delta sigma weight residual 0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N VAL W 99 " pdb=" H VAL W 99 " ideal model delta sigma weight residual 0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N VAL O 99 " pdb=" H VAL O 99 " ideal model delta sigma weight residual 0.860 1.107 -0.247 2.00e-02 2.50e+03 1.53e+02 ... (remaining 65801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.00: 117993 6.00 - 11.99: 853 11.99 - 17.99: 286 17.99 - 23.99: 78 23.99 - 29.99: 52 Bond angle restraints: 119262 Sorted by residual: angle pdb=" N THR Y 103 " pdb=" CA THR Y 103 " pdb=" C THR Y 103 " ideal model delta sigma weight residual 111.07 130.07 -19.00 1.07e+00 8.73e-01 3.15e+02 angle pdb=" N THR K 103 " pdb=" CA THR K 103 " pdb=" C THR K 103 " ideal model delta sigma weight residual 111.07 130.04 -18.97 1.07e+00 8.73e-01 3.14e+02 angle pdb=" N THR I 103 " pdb=" CA THR I 103 " pdb=" C THR I 103 " ideal model delta sigma weight residual 111.07 130.02 -18.95 1.07e+00 8.73e-01 3.13e+02 angle pdb=" N THR S 103 " pdb=" CA THR S 103 " pdb=" C THR S 103 " ideal model delta sigma weight residual 111.07 130.00 -18.93 1.07e+00 8.73e-01 3.13e+02 angle pdb=" N THR C 103 " pdb=" CA THR C 103 " pdb=" C THR C 103 " ideal model delta sigma weight residual 111.07 129.98 -18.91 1.07e+00 8.73e-01 3.12e+02 ... (remaining 119257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 28283 15.31 - 30.61: 1420 30.61 - 45.92: 755 45.92 - 61.22: 508 61.22 - 76.53: 52 Dihedral angle restraints: 31018 sinusoidal: 16822 harmonic: 14196 Sorted by residual: dihedral pdb=" CA ASP G 156 " pdb=" C ASP G 156 " pdb=" N GLY G 157 " pdb=" CA GLY G 157 " ideal model delta harmonic sigma weight residual -180.00 -145.06 -34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP T 156 " pdb=" C ASP T 156 " pdb=" N GLY T 157 " pdb=" CA GLY T 157 " ideal model delta harmonic sigma weight residual 180.00 -145.08 -34.92 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP J 156 " pdb=" C ASP J 156 " pdb=" N GLY J 157 " pdb=" CA GLY J 157 " ideal model delta harmonic sigma weight residual -180.00 -145.17 -34.83 0 5.00e+00 4.00e-02 4.85e+01 ... (remaining 31015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4387 0.083 - 0.167: 629 0.167 - 0.250: 118 0.250 - 0.333: 81 0.333 - 0.416: 89 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA THR U 103 " pdb=" N THR U 103 " pdb=" C THR U 103 " pdb=" CB THR U 103 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA THR E 103 " pdb=" N THR E 103 " pdb=" C THR E 103 " pdb=" CB THR E 103 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA GLN D 110 " pdb=" N GLN D 110 " pdb=" C GLN D 110 " pdb=" CB GLN D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 5301 not shown) Planarity restraints: 9594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" N VAL H 99 " 0.376 2.00e-02 2.50e+03 pdb=" CA VAL H 99 " -0.121 2.00e-02 2.50e+03 pdb=" H VAL H 99 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" N VAL D 99 " 0.376 2.00e-02 2.50e+03 pdb=" CA VAL D 99 " -0.122 2.00e-02 2.50e+03 pdb=" H VAL D 99 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 98 " 0.132 2.00e-02 2.50e+03 2.17e-01 4.71e+02 pdb=" N VAL Y 99 " -0.376 2.00e-02 2.50e+03 pdb=" CA VAL Y 99 " 0.121 2.00e-02 2.50e+03 pdb=" H VAL Y 99 " 0.123 2.00e-02 2.50e+03 ... (remaining 9591 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 306 1.84 - 2.53: 61893 2.53 - 3.22: 212773 3.22 - 3.91: 279988 3.91 - 4.60: 454291 Nonbonded interactions: 1009251 Sorted by model distance: nonbonded pdb=" OD1 ASP I 53 " pdb=" HH TYR B 22 " model vdw 1.154 2.450 nonbonded pdb=" OD1 ASP C 53 " pdb=" HH TYR O 22 " model vdw 1.154 2.450 nonbonded pdb=" HH TYR F 22 " pdb=" OD1 ASP V 53 " model vdw 1.155 2.450 nonbonded pdb=" OD1 ASP F 53 " pdb=" HH TYR R 22 " model vdw 1.155 2.450 nonbonded pdb=" HH TYR G 22 " pdb=" OD1 ASP W 53 " model vdw 1.155 2.450 ... (remaining 1009246 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' selection = chain 'Y' selection = chain 'Z' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.890 Extract box with map and model: 1.770 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 100.140 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.045 32760 Z= 0.479 Angle : 1.915 19.693 44512 Z= 1.271 Chirality : 0.085 0.416 5304 Planarity : 0.005 0.049 5512 Dihedral : 13.178 76.527 11596 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.79 % Allowed : 5.30 % Favored : 90.91 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -2.21 (0.11), residues: 4212 helix: -0.54 (0.14), residues: 1170 sheet: -2.03 (0.12), residues: 1170 loop : -1.54 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 92 PHE 0.024 0.004 PHE H 1 TYR 0.020 0.003 TYR Q 73 ARG 0.007 0.001 ARG O 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2436 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 2306 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 PHE cc_start: 0.8894 (m-10) cc_final: 0.8638 (m-10) REVERT: I 45 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8531 (tp-100) REVERT: I 81 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9265 (mm-30) REVERT: I 112 LEU cc_start: 0.8985 (mp) cc_final: 0.8740 (mm) REVERT: I 143 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8907 (tptt) REVERT: A 112 LEU cc_start: 0.9162 (mp) cc_final: 0.8844 (mm) REVERT: B 86 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9178 (tppt) REVERT: B 112 LEU cc_start: 0.8991 (mp) cc_final: 0.8724 (mm) REVERT: B 139 GLU cc_start: 0.9527 (tt0) cc_final: 0.9287 (tt0) REVERT: C 34 LYS cc_start: 0.9507 (tptt) cc_final: 0.9223 (tppt) REVERT: D 25 LEU cc_start: 0.9616 (mt) cc_final: 0.9212 (mt) REVERT: D 30 PHE cc_start: 0.9382 (t80) cc_final: 0.8988 (t80) REVERT: D 36 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (mm-40) REVERT: D 53 ASP cc_start: 0.9388 (t70) cc_final: 0.9105 (t0) REVERT: E 112 LEU cc_start: 0.8929 (mp) cc_final: 0.8706 (mm) REVERT: F 30 PHE cc_start: 0.9453 (t80) cc_final: 0.9250 (t80) REVERT: F 112 LEU cc_start: 0.9176 (mp) cc_final: 0.8882 (mm) REVERT: G 86 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9131 (tppt) REVERT: G 112 LEU cc_start: 0.9118 (mp) cc_final: 0.8856 (mm) REVERT: H 86 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (tppt) REVERT: H 112 LEU cc_start: 0.9001 (mp) cc_final: 0.8788 (mm) REVERT: J 25 LEU cc_start: 0.9611 (mt) cc_final: 0.9116 (mt) REVERT: J 30 PHE cc_start: 0.9411 (t80) cc_final: 0.9015 (t80) REVERT: K 34 LYS cc_start: 0.9481 (tptt) cc_final: 0.9197 (tppt) REVERT: K 112 LEU cc_start: 0.8949 (mp) cc_final: 0.8685 (mm) REVERT: L 13 PHE cc_start: 0.8939 (m-10) cc_final: 0.8677 (m-10) REVERT: L 45 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8715 (tp-100) REVERT: L 143 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8876 (tptt) REVERT: N 25 LEU cc_start: 0.9561 (mt) cc_final: 0.9274 (mt) REVERT: N 86 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9165 (tppt) REVERT: N 112 LEU cc_start: 0.9077 (mp) cc_final: 0.8834 (mm) REVERT: O 34 LYS cc_start: 0.9535 (tptt) cc_final: 0.9279 (tppt) REVERT: O 45 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8853 (tp40) REVERT: O 112 LEU cc_start: 0.8952 (mp) cc_final: 0.8727 (mm) REVERT: P 22 TYR cc_start: 0.9284 (t80) cc_final: 0.8833 (t80) REVERT: P 30 PHE cc_start: 0.9345 (t80) cc_final: 0.8949 (t80) REVERT: P 44 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9146 (ttmt) REVERT: Q 30 PHE cc_start: 0.9383 (t80) cc_final: 0.9170 (t80) REVERT: Q 34 LYS cc_start: 0.9480 (tptt) cc_final: 0.9176 (tppt) REVERT: Q 86 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (tppt) REVERT: Q 112 LEU cc_start: 0.8940 (mp) cc_final: 0.8672 (mm) REVERT: R 25 LEU cc_start: 0.9330 (mt) cc_final: 0.9064 (mt) REVERT: R 86 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9096 (tppt) REVERT: S 86 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9097 (tppt) REVERT: T 13 PHE cc_start: 0.8881 (m-10) cc_final: 0.8619 (m-10) REVERT: T 36 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: T 40 TYR cc_start: 0.8944 (m-10) cc_final: 0.8448 (m-80) REVERT: T 112 LEU cc_start: 0.9026 (mp) cc_final: 0.8793 (mm) REVERT: T 143 LYS cc_start: 0.9325 (ttpp) cc_final: 0.8840 (tptt) REVERT: U 30 PHE cc_start: 0.9461 (t80) cc_final: 0.9152 (t80) REVERT: U 36 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (mm-40) REVERT: U 45 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8885 (tp-100) REVERT: U 86 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9082 (tppt) REVERT: U 112 LEU cc_start: 0.8902 (mp) cc_final: 0.8659 (mm) REVERT: V 30 PHE cc_start: 0.9544 (t80) cc_final: 0.9337 (t80) REVERT: V 112 LEU cc_start: 0.9076 (mp) cc_final: 0.8754 (mm) REVERT: V 147 SER cc_start: 0.9230 (m) cc_final: 0.8834 (p) REVERT: W 45 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8797 (tp-100) REVERT: W 86 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9183 (tppt) REVERT: W 112 LEU cc_start: 0.9022 (mp) cc_final: 0.8702 (mm) REVERT: W 136 PHE cc_start: 0.8661 (p90) cc_final: 0.8447 (p90) REVERT: X 44 LYS cc_start: 0.9262 (ttmt) cc_final: 0.9061 (ttmt) REVERT: X 45 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8833 (tp-100) REVERT: X 112 LEU cc_start: 0.9143 (mp) cc_final: 0.8890 (mm) REVERT: Y 25 LEU cc_start: 0.9617 (mt) cc_final: 0.9223 (mt) REVERT: Y 30 PHE cc_start: 0.9476 (t80) cc_final: 0.9152 (t80) REVERT: Y 112 LEU cc_start: 0.8994 (mp) cc_final: 0.8748 (mm) REVERT: Y 147 SER cc_start: 0.9357 (m) cc_final: 0.8972 (p) REVERT: Z 36 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8818 (mm-40) REVERT: Z 86 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9098 (tppt) REVERT: Z 112 LEU cc_start: 0.8955 (mp) cc_final: 0.8682 (mm) outliers start: 130 outliers final: 57 residues processed: 2332 average time/residue: 0.8657 time to fit residues: 3207.7274 Evaluate side-chains 2162 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 2091 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain A residue 1 PHE Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 1 PHE Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 1 PHE Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain F residue 1 PHE Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 86 LYS Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 36 GLN Chi-restraints excluded: chain U residue 86 LYS Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain X residue 1 PHE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 1 PHE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 86 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 326 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 ASN A 36 GLN A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 113 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN D 113 ASN E 83 GLN ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN H 109 ASN ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 ASN J 113 ASN K 83 GLN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 109 ASN L 113 ASN ** M 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN O 109 ASN ** P 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN P 113 ASN ** Q 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN S 109 ASN S 113 ASN T 109 ASN T 113 ASN U 33 GLN U 109 ASN W 33 GLN ** W 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN X 113 ASN ** Y 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 109 ASN ** Z 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32760 Z= 0.288 Angle : 0.703 6.677 44512 Z= 0.394 Chirality : 0.047 0.165 5304 Planarity : 0.004 0.037 5512 Dihedral : 8.847 59.768 4752 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.44 % Allowed : 21.91 % Favored : 74.65 % 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: -1.73 (0.11), residues: 4212 helix: 0.75 (0.13), residues: 1144 sheet: -1.82 (0.11), residues: 1274 loop : -1.80 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 92 PHE 0.019 0.002 PHE E 136 TYR 0.017 0.002 TYR N 73 ARG 0.003 0.001 ARG W 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2283 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 2165 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 22 TYR cc_start: 0.9117 (t80) cc_final: 0.8509 (t80) REVERT: I 90 TYR cc_start: 0.8386 (m-80) cc_final: 0.8183 (m-80) REVERT: I 119 LYS cc_start: 0.9350 (ttpp) cc_final: 0.9095 (tttm) REVERT: I 143 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8799 (tptt) REVERT: A 25 LEU cc_start: 0.9507 (mt) cc_final: 0.8801 (mt) REVERT: B 45 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8776 (tp-100) REVERT: C 45 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8888 (tp-100) REVERT: C 57 TYR cc_start: 0.8609 (m-80) cc_final: 0.8381 (m-80) REVERT: E 91 LEU cc_start: 0.9158 (mt) cc_final: 0.8895 (mt) REVERT: F 22 TYR cc_start: 0.9121 (t80) cc_final: 0.8770 (t80) REVERT: F 25 LEU cc_start: 0.9494 (mt) cc_final: 0.8951 (mt) REVERT: G 30 PHE cc_start: 0.9432 (t80) cc_final: 0.9151 (t80) REVERT: G 45 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8768 (tp-100) REVERT: G 152 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8525 (mmt90) REVERT: H 45 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8841 (tp-100) REVERT: J 34 LYS cc_start: 0.9487 (tptt) cc_final: 0.9265 (mmmm) REVERT: J 83 GLN cc_start: 0.8853 (mm110) cc_final: 0.8491 (mm110) REVERT: J 119 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8899 (tttp) REVERT: L 25 LEU cc_start: 0.9428 (mt) cc_final: 0.9132 (mt) REVERT: L 143 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8840 (tptt) REVERT: N 24 MET cc_start: 0.8235 (ttt) cc_final: 0.7980 (ttt) REVERT: P 34 LYS cc_start: 0.9509 (tptt) cc_final: 0.9275 (mmmm) REVERT: P 83 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8562 (mm110) REVERT: Q 83 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8561 (mm110) REVERT: Q 86 LYS cc_start: 0.9280 (ttmm) cc_final: 0.9023 (tppt) REVERT: R 25 LEU cc_start: 0.9200 (mt) cc_final: 0.8823 (mt) REVERT: R 81 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9033 (mm-30) REVERT: R 83 GLN cc_start: 0.9013 (mm110) cc_final: 0.8595 (mm110) REVERT: T 22 TYR cc_start: 0.9260 (t80) cc_final: 0.8859 (t80) REVERT: T 73 TYR cc_start: 0.8511 (m-80) cc_final: 0.8193 (m-80) REVERT: T 119 LYS cc_start: 0.9296 (ttpp) cc_final: 0.9070 (mtpp) REVERT: T 143 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8807 (tptt) REVERT: U 45 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8739 (tp-100) REVERT: U 91 LEU cc_start: 0.9101 (mt) cc_final: 0.8855 (mt) REVERT: V 22 TYR cc_start: 0.9129 (t80) cc_final: 0.8888 (t80) REVERT: V 34 LYS cc_start: 0.9512 (tptt) cc_final: 0.9282 (mmmm) REVERT: W 22 TYR cc_start: 0.9110 (t80) cc_final: 0.8570 (t80) REVERT: W 30 PHE cc_start: 0.9508 (t80) cc_final: 0.9228 (t80) REVERT: W 119 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9021 (tttp) REVERT: W 136 PHE cc_start: 0.8659 (p90) cc_final: 0.8375 (p90) REVERT: W 152 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8472 (mmt-90) REVERT: X 22 TYR cc_start: 0.9126 (t80) cc_final: 0.8808 (t80) REVERT: X 44 LYS cc_start: 0.9218 (ttmt) cc_final: 0.9013 (ttmt) REVERT: X 45 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8836 (tp-100) REVERT: Y 22 TYR cc_start: 0.9052 (t80) cc_final: 0.8767 (t80) REVERT: Y 34 LYS cc_start: 0.9460 (tptt) cc_final: 0.9245 (mmmm) REVERT: Z 81 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8966 (mm-30) REVERT: Z 83 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8942 (mm110) REVERT: Z 91 LEU cc_start: 0.9132 (mt) cc_final: 0.8879 (mt) REVERT: Z 119 LYS cc_start: 0.9170 (ttpp) cc_final: 0.8883 (mtpp) outliers start: 118 outliers final: 69 residues processed: 2192 average time/residue: 0.8960 time to fit residues: 3117.2838 Evaluate side-chains 2121 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 2052 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 105 ILE Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 378 optimal weight: 0.7980 chunk 408 optimal weight: 9.9990 chunk 337 optimal weight: 1.9990 chunk 375 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 109 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN H 109 ASN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN N 83 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN R 109 ASN S 109 ASN T 96 ASN ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 109 ASN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32760 Z= 0.277 Angle : 0.640 4.938 44512 Z= 0.355 Chirality : 0.045 0.160 5304 Planarity : 0.004 0.032 5512 Dihedral : 6.152 57.855 4601 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.26 % Allowed : 29.46 % Favored : 67.28 % 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: -1.33 (0.12), residues: 4212 helix: 1.28 (0.13), residues: 1144 sheet: -1.52 (0.12), residues: 1274 loop : -1.77 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 92 PHE 0.019 0.002 PHE N 20 TYR 0.020 0.002 TYR Y 73 ARG 0.004 0.001 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2188 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 2076 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 29 PHE cc_start: 0.9089 (m-10) cc_final: 0.8852 (m-80) REVERT: I 40 TYR cc_start: 0.8941 (m-10) cc_final: 0.8652 (m-10) REVERT: I 90 TYR cc_start: 0.8500 (m-80) cc_final: 0.8248 (m-80) REVERT: I 143 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8798 (tptt) REVERT: A 25 LEU cc_start: 0.9516 (mt) cc_final: 0.9202 (mt) REVERT: B 136 PHE cc_start: 0.8723 (p90) cc_final: 0.8298 (p90) REVERT: B 152 ARG cc_start: 0.8887 (mmt-90) cc_final: 0.8501 (mmt-90) REVERT: C 45 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8856 (tp-100) REVERT: E 45 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8698 (tp-100) REVERT: G 45 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8668 (tp-100) REVERT: H 45 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8768 (tp-100) REVERT: H 83 GLN cc_start: 0.8621 (mm110) cc_final: 0.8410 (mm110) REVERT: H 86 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8806 (tppt) REVERT: J 34 LYS cc_start: 0.9541 (tptt) cc_final: 0.9307 (mmmm) REVERT: J 152 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8736 (mmt-90) REVERT: K 83 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8010 (mm110) REVERT: K 147 SER cc_start: 0.9324 (m) cc_final: 0.8990 (p) REVERT: L 71 TYR cc_start: 0.9059 (m-10) cc_final: 0.8696 (m-10) REVERT: L 143 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8853 (tptt) REVERT: L 154 LEU cc_start: 0.8704 (mt) cc_final: 0.8501 (mm) REVERT: N 30 PHE cc_start: 0.9397 (t80) cc_final: 0.9177 (t80) REVERT: O 83 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8605 (mm-40) REVERT: P 73 TYR cc_start: 0.8600 (m-80) cc_final: 0.8340 (m-80) REVERT: Q 29 PHE cc_start: 0.9115 (m-10) cc_final: 0.8817 (m-10) REVERT: Q 75 LYS cc_start: 0.8923 (ptpt) cc_final: 0.8644 (ptmm) REVERT: Q 83 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8781 (mm110) REVERT: R 29 PHE cc_start: 0.9018 (m-10) cc_final: 0.8779 (m-10) REVERT: R 86 LYS cc_start: 0.9365 (ttmm) cc_final: 0.9146 (tppt) REVERT: S 86 LYS cc_start: 0.9281 (ttmm) cc_final: 0.9017 (tppt) REVERT: T 22 TYR cc_start: 0.9218 (t80) cc_final: 0.8978 (t80) REVERT: T 40 TYR cc_start: 0.8958 (m-10) cc_final: 0.8458 (m-10) REVERT: T 119 LYS cc_start: 0.9255 (ttpp) cc_final: 0.9001 (mtpp) REVERT: T 136 PHE cc_start: 0.8930 (p90) cc_final: 0.8724 (p90) REVERT: T 143 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8847 (tptt) REVERT: U 45 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8698 (tp-100) REVERT: U 72 PHE cc_start: 0.8613 (p90) cc_final: 0.8408 (p90) REVERT: U 81 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8919 (mm-30) REVERT: U 86 LYS cc_start: 0.9229 (ttmm) cc_final: 0.9029 (tppt) REVERT: V 40 TYR cc_start: 0.8987 (m-10) cc_final: 0.8643 (m-80) REVERT: W 22 TYR cc_start: 0.9050 (t80) cc_final: 0.8473 (t80) REVERT: X 22 TYR cc_start: 0.9146 (t80) cc_final: 0.8868 (t80) REVERT: X 45 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8752 (tp-100) REVERT: X 71 TYR cc_start: 0.9043 (m-10) cc_final: 0.8727 (m-10) REVERT: X 83 GLN cc_start: 0.8862 (mm110) cc_final: 0.8592 (mm110) REVERT: X 139 GLU cc_start: 0.9506 (tt0) cc_final: 0.9297 (tt0) REVERT: Y 22 TYR cc_start: 0.9027 (t80) cc_final: 0.8703 (t80) REVERT: Y 152 ARG cc_start: 0.8989 (mmt-90) cc_final: 0.8724 (mmt90) REVERT: Z 45 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8743 (tp-100) REVERT: Z 81 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9028 (mm-30) REVERT: Z 147 SER cc_start: 0.9301 (m) cc_final: 0.9097 (p) outliers start: 112 outliers final: 73 residues processed: 2092 average time/residue: 0.9328 time to fit residues: 3104.0875 Evaluate side-chains 2103 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 2030 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain Q residue 135 LYS Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 379 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN F 36 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 ASN L 36 GLN L 83 GLN O 36 GLN T 109 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN V 83 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Y 113 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 32760 Z= 0.371 Angle : 0.651 5.636 44512 Z= 0.367 Chirality : 0.045 0.150 5304 Planarity : 0.004 0.032 5512 Dihedral : 5.800 59.285 4592 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.14 % Allowed : 31.47 % Favored : 64.39 % 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: -1.38 (0.12), residues: 4212 helix: 1.67 (0.13), residues: 1144 sheet: -1.67 (0.13), residues: 1274 loop : -2.05 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 92 PHE 0.032 0.002 PHE T 29 TYR 0.024 0.002 TYR I 40 ARG 0.005 0.001 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2186 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 2044 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 29 PHE cc_start: 0.9119 (m-10) cc_final: 0.8904 (m-80) REVERT: I 44 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9210 (mtmt) REVERT: I 143 LYS cc_start: 0.9236 (ttpp) cc_final: 0.8931 (tptt) REVERT: A 25 LEU cc_start: 0.9492 (mt) cc_final: 0.9184 (mt) REVERT: A 72 PHE cc_start: 0.8839 (p90) cc_final: 0.8596 (p90) REVERT: B 147 SER cc_start: 0.9382 (m) cc_final: 0.9114 (p) REVERT: B 152 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8461 (mmt90) REVERT: C 45 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8808 (tp-100) REVERT: C 83 GLN cc_start: 0.8850 (mm110) cc_final: 0.8642 (mm110) REVERT: E 25 LEU cc_start: 0.9471 (mt) cc_final: 0.9210 (mt) REVERT: E 45 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8733 (tp-100) REVERT: H 45 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8836 (tp-100) REVERT: J 34 LYS cc_start: 0.9612 (tptt) cc_final: 0.9325 (mmmm) REVERT: J 36 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8925 (tt0) REVERT: J 147 SER cc_start: 0.9460 (m) cc_final: 0.9171 (p) REVERT: K 36 GLN cc_start: 0.9067 (mt0) cc_final: 0.8840 (mm-40) REVERT: K 45 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8704 (tp-100) REVERT: K 83 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8241 (mm110) REVERT: L 45 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8577 (tp-100) REVERT: L 71 TYR cc_start: 0.9098 (m-10) cc_final: 0.8887 (m-10) REVERT: L 143 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8878 (tptt) REVERT: M 29 PHE cc_start: 0.9114 (m-10) cc_final: 0.8902 (m-80) REVERT: N 34 LYS cc_start: 0.9616 (tptt) cc_final: 0.9356 (mmmm) REVERT: N 83 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8482 (mm110) REVERT: N 86 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8768 (tppt) REVERT: P 34 LYS cc_start: 0.9607 (tptt) cc_final: 0.9331 (mmmm) REVERT: P 147 SER cc_start: 0.9366 (m) cc_final: 0.9088 (p) REVERT: Q 25 LEU cc_start: 0.9087 (mt) cc_final: 0.8677 (mt) REVERT: Q 29 PHE cc_start: 0.9190 (m-10) cc_final: 0.8960 (m-10) REVERT: Q 86 LYS cc_start: 0.9299 (ttmm) cc_final: 0.8967 (tppt) REVERT: R 81 GLU cc_start: 0.9265 (mm-30) cc_final: 0.9052 (mm-30) REVERT: R 83 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8575 (mm110) REVERT: R 86 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9152 (tppt) REVERT: S 36 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6753 (mm-40) REVERT: S 84 ASP cc_start: 0.9276 (t0) cc_final: 0.9015 (t0) REVERT: S 86 LYS cc_start: 0.9335 (ttmm) cc_final: 0.9044 (tppt) REVERT: T 36 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8812 (mm-40) REVERT: T 119 LYS cc_start: 0.9307 (ttpp) cc_final: 0.9036 (mtpp) REVERT: T 143 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8902 (tptt) REVERT: U 40 TYR cc_start: 0.9046 (m-10) cc_final: 0.8731 (m-10) REVERT: U 45 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8750 (tp-100) REVERT: W 22 TYR cc_start: 0.9040 (t80) cc_final: 0.8630 (t80) REVERT: W 119 LYS cc_start: 0.9341 (ttpp) cc_final: 0.8927 (mtpp) REVERT: X 22 TYR cc_start: 0.9166 (t80) cc_final: 0.8940 (t80) REVERT: X 45 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8772 (tp-100) REVERT: X 71 TYR cc_start: 0.9138 (m-10) cc_final: 0.8878 (m-10) REVERT: X 147 SER cc_start: 0.9212 (m) cc_final: 0.8895 (p) REVERT: Y 22 TYR cc_start: 0.9072 (t80) cc_final: 0.8773 (t80) REVERT: Y 36 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9059 (tt0) REVERT: Y 152 ARG cc_start: 0.8969 (mmt-90) cc_final: 0.8646 (mmt90) REVERT: Z 45 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8787 (tp-100) REVERT: Z 84 ASP cc_start: 0.9338 (t0) cc_final: 0.9099 (t0) REVERT: Z 86 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8846 (ttpp) outliers start: 142 outliers final: 100 residues processed: 2092 average time/residue: 0.9140 time to fit residues: 3036.3816 Evaluate side-chains 2083 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1979 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain Q residue 147 SER Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 105 ILE Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 36 GLN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN N 36 GLN N 113 ASN U 36 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN W 36 GLN X 49 ASN X 113 ASN ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 32760 Z= 0.324 Angle : 0.633 6.690 44512 Z= 0.353 Chirality : 0.045 0.166 5304 Planarity : 0.004 0.033 5512 Dihedral : 5.542 57.120 4585 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.70 % Allowed : 33.83 % Favored : 62.47 % 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: -1.49 (0.12), residues: 4212 helix: 1.70 (0.13), residues: 1144 sheet: -1.77 (0.13), residues: 1274 loop : -2.17 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 92 PHE 0.024 0.002 PHE W 136 TYR 0.029 0.002 TYR E 73 ARG 0.005 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2144 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 2017 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 143 LYS cc_start: 0.9251 (ttpp) cc_final: 0.8942 (tptt) REVERT: B 136 PHE cc_start: 0.8767 (p90) cc_final: 0.8537 (p90) REVERT: B 147 SER cc_start: 0.9335 (m) cc_final: 0.9080 (p) REVERT: B 152 ARG cc_start: 0.8740 (mmt-90) cc_final: 0.8109 (mmt-90) REVERT: C 34 LYS cc_start: 0.9635 (tptt) cc_final: 0.9378 (tppt) REVERT: C 45 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8677 (tp-100) REVERT: C 83 GLN cc_start: 0.8901 (mm110) cc_final: 0.8618 (mm110) REVERT: D 36 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8937 (mm-40) REVERT: E 25 LEU cc_start: 0.9493 (mt) cc_final: 0.9217 (mt) REVERT: E 45 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8678 (tp-100) REVERT: E 83 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7884 (mm110) REVERT: F 72 PHE cc_start: 0.8759 (p90) cc_final: 0.8532 (p90) REVERT: G 34 LYS cc_start: 0.9603 (tptt) cc_final: 0.9394 (mmmm) REVERT: H 45 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8714 (tp-100) REVERT: H 86 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8884 (tppt) REVERT: J 25 LEU cc_start: 0.9427 (mt) cc_final: 0.9223 (mt) REVERT: J 36 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8937 (tt0) REVERT: J 83 GLN cc_start: 0.8625 (mm110) cc_final: 0.8382 (mm110) REVERT: J 147 SER cc_start: 0.9378 (m) cc_final: 0.9122 (p) REVERT: K 45 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8657 (tp-100) REVERT: K 83 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8241 (mm110) REVERT: K 86 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8996 (tppt) REVERT: L 45 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8581 (tp-100) REVERT: L 119 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8990 (tttp) REVERT: L 143 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8891 (tptt) REVERT: O 83 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8879 (mm110) REVERT: P 36 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8678 (tp40) REVERT: P 40 TYR cc_start: 0.8495 (m-10) cc_final: 0.8254 (m-10) REVERT: P 147 SER cc_start: 0.9363 (m) cc_final: 0.9088 (p) REVERT: Q 25 LEU cc_start: 0.9118 (mt) cc_final: 0.8737 (mt) REVERT: Q 29 PHE cc_start: 0.9185 (m-10) cc_final: 0.8957 (m-10) REVERT: Q 119 LYS cc_start: 0.9279 (ttpp) cc_final: 0.9070 (tttp) REVERT: R 29 PHE cc_start: 0.9127 (m-10) cc_final: 0.8881 (m-10) REVERT: R 81 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9021 (mm-30) REVERT: R 83 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8620 (mm110) REVERT: R 86 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9101 (tppt) REVERT: S 86 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8827 (tppt) REVERT: T 36 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8600 (mm-40) REVERT: T 119 LYS cc_start: 0.9296 (ttpp) cc_final: 0.9039 (mtpp) REVERT: T 143 LYS cc_start: 0.9155 (ttpp) cc_final: 0.8899 (tptt) REVERT: T 152 ARG cc_start: 0.8942 (mmt-90) cc_final: 0.8595 (mmt90) REVERT: U 22 TYR cc_start: 0.9145 (t80) cc_final: 0.8787 (t80) REVERT: U 45 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8783 (tp-100) REVERT: U 83 GLN cc_start: 0.8696 (mm110) cc_final: 0.8387 (mm110) REVERT: U 136 PHE cc_start: 0.8812 (p90) cc_final: 0.8605 (p90) REVERT: V 22 TYR cc_start: 0.8858 (t80) cc_final: 0.8615 (t80) REVERT: V 29 PHE cc_start: 0.8825 (m-10) cc_final: 0.8620 (m-10) REVERT: W 22 TYR cc_start: 0.9059 (t80) cc_final: 0.8663 (t80) REVERT: X 22 TYR cc_start: 0.9167 (t80) cc_final: 0.8917 (t80) REVERT: X 45 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8706 (tp-100) REVERT: X 71 TYR cc_start: 0.9113 (m-10) cc_final: 0.8889 (m-10) REVERT: X 143 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8732 (ttpp) REVERT: X 147 SER cc_start: 0.9314 (m) cc_final: 0.9057 (p) REVERT: Y 22 TYR cc_start: 0.9097 (t80) cc_final: 0.8727 (t80) REVERT: Y 36 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9095 (tt0) REVERT: Z 45 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8698 (tp-100) REVERT: Z 84 ASP cc_start: 0.9254 (t0) cc_final: 0.8973 (t0) REVERT: Z 111 GLN cc_start: 0.9266 (mp10) cc_final: 0.8915 (mm-40) REVERT: Z 112 LEU cc_start: 0.9248 (mm) cc_final: 0.8846 (mm) outliers start: 127 outliers final: 109 residues processed: 2058 average time/residue: 0.8722 time to fit residues: 2847.2433 Evaluate side-chains 2093 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1981 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain Q residue 147 SER Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 105 ILE Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 402 optimal weight: 9.9990 chunk 334 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN B 49 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN F 36 GLN G 49 ASN J 109 ASN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN X 113 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32760 Z= 0.218 Angle : 0.599 8.521 44512 Z= 0.326 Chirality : 0.045 0.177 5304 Planarity : 0.004 0.038 5512 Dihedral : 5.379 58.497 4583 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.06 % Allowed : 34.82 % Favored : 62.12 % 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: -1.27 (0.12), residues: 4212 helix: 1.93 (0.13), residues: 1144 sheet: -1.68 (0.14), residues: 1144 loop : -2.06 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 92 PHE 0.028 0.002 PHE I 29 TYR 0.025 0.002 TYR B 40 ARG 0.006 0.001 ARG Y 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2161 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 2056 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9172 (mtmt) REVERT: I 119 LYS cc_start: 0.9343 (ttpp) cc_final: 0.8927 (mtpp) REVERT: I 143 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8855 (tptt) REVERT: B 86 LYS cc_start: 0.9168 (ttmm) cc_final: 0.8777 (tppt) REVERT: B 136 PHE cc_start: 0.8680 (p90) cc_final: 0.8471 (p90) REVERT: B 147 SER cc_start: 0.9266 (m) cc_final: 0.9024 (p) REVERT: B 152 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8094 (mmt-90) REVERT: C 45 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8563 (tp-100) REVERT: C 83 GLN cc_start: 0.8813 (mm110) cc_final: 0.8548 (mm110) REVERT: E 25 LEU cc_start: 0.9485 (mt) cc_final: 0.9241 (mt) REVERT: E 40 TYR cc_start: 0.8656 (m-10) cc_final: 0.8110 (m-80) REVERT: E 45 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8443 (tp-100) REVERT: F 72 PHE cc_start: 0.8702 (p90) cc_final: 0.8498 (p90) REVERT: G 34 LYS cc_start: 0.9568 (tptt) cc_final: 0.9310 (mmmm) REVERT: H 45 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8562 (tp-100) REVERT: J 25 LEU cc_start: 0.9368 (mt) cc_final: 0.9160 (mt) REVERT: J 36 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9007 (tt0) REVERT: J 83 GLN cc_start: 0.8571 (mm110) cc_final: 0.8353 (mm110) REVERT: K 40 TYR cc_start: 0.8445 (m-10) cc_final: 0.7973 (m-80) REVERT: K 45 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8399 (tp-100) REVERT: K 83 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8224 (mm110) REVERT: K 86 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8709 (tppt) REVERT: K 147 SER cc_start: 0.9266 (m) cc_final: 0.8968 (p) REVERT: L 45 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8478 (tp-100) REVERT: L 83 GLN cc_start: 0.8603 (mm110) cc_final: 0.8386 (mm110) REVERT: L 119 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8965 (tttp) REVERT: L 143 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8895 (tptt) REVERT: P 36 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8961 (mm-40) REVERT: P 83 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8706 (mm110) REVERT: Q 25 LEU cc_start: 0.9094 (mt) cc_final: 0.8701 (mt) REVERT: Q 29 PHE cc_start: 0.9165 (m-10) cc_final: 0.8910 (m-10) REVERT: Q 83 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8761 (mm110) REVERT: Q 119 LYS cc_start: 0.9209 (ttpp) cc_final: 0.8975 (tttp) REVERT: R 29 PHE cc_start: 0.9105 (m-10) cc_final: 0.8904 (m-10) REVERT: R 86 LYS cc_start: 0.9259 (ttmm) cc_final: 0.9005 (tppt) REVERT: S 86 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8796 (tppt) REVERT: T 119 LYS cc_start: 0.9239 (ttpp) cc_final: 0.9015 (mtpp) REVERT: T 143 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8883 (tptt) REVERT: T 152 ARG cc_start: 0.8826 (mmt-90) cc_final: 0.8534 (mmt90) REVERT: U 22 TYR cc_start: 0.9086 (t80) cc_final: 0.8739 (t80) REVERT: U 45 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8575 (tp-100) REVERT: V 22 TYR cc_start: 0.8825 (t80) cc_final: 0.8597 (t80) REVERT: V 45 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8436 (tp-100) REVERT: W 22 TYR cc_start: 0.9022 (t80) cc_final: 0.8666 (t80) REVERT: W 119 LYS cc_start: 0.9309 (ttpp) cc_final: 0.9028 (tttp) REVERT: X 22 TYR cc_start: 0.9153 (t80) cc_final: 0.8946 (t80) REVERT: X 143 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8680 (ttpp) REVERT: Y 22 TYR cc_start: 0.9053 (t80) cc_final: 0.8607 (t80) REVERT: Z 45 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8483 (tp-100) REVERT: Z 84 ASP cc_start: 0.9203 (t0) cc_final: 0.8933 (t0) REVERT: Z 86 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8735 (tppt) outliers start: 105 outliers final: 88 residues processed: 2086 average time/residue: 0.9076 time to fit residues: 3009.7514 Evaluate side-chains 2092 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 2001 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 49 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 overall best weight: 5.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN R 83 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32760 Z= 0.368 Angle : 0.661 8.844 44512 Z= 0.370 Chirality : 0.045 0.160 5304 Planarity : 0.004 0.036 5512 Dihedral : 5.404 59.206 4582 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.46 % Allowed : 36.04 % Favored : 59.50 % 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: -1.44 (0.12), residues: 4212 helix: 1.83 (0.13), residues: 1170 sheet: -1.82 (0.14), residues: 1144 loop : -2.22 (0.12), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 92 PHE 0.033 0.002 PHE I 29 TYR 0.030 0.002 TYR Z 73 ARG 0.006 0.001 ARG Z 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2143 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1990 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9228 (mtmt) REVERT: I 119 LYS cc_start: 0.9379 (ttpp) cc_final: 0.8891 (mtpp) REVERT: I 143 LYS cc_start: 0.9287 (ttpp) cc_final: 0.8957 (tptt) REVERT: A 57 TYR cc_start: 0.8671 (m-80) cc_final: 0.8365 (m-80) REVERT: B 72 PHE cc_start: 0.8832 (p90) cc_final: 0.8611 (p90) REVERT: B 86 LYS cc_start: 0.9289 (ttmm) cc_final: 0.8929 (tppt) REVERT: B 136 PHE cc_start: 0.8766 (p90) cc_final: 0.8533 (p90) REVERT: C 29 PHE cc_start: 0.9213 (m-80) cc_final: 0.8958 (m-80) REVERT: C 45 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8609 (tp-100) REVERT: C 83 GLN cc_start: 0.8905 (mm110) cc_final: 0.8606 (mm110) REVERT: C 147 SER cc_start: 0.9270 (m) cc_final: 0.9063 (p) REVERT: D 36 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8925 (tp40) REVERT: D 40 TYR cc_start: 0.8516 (m-10) cc_final: 0.8313 (m-10) REVERT: E 20 PHE cc_start: 0.8804 (t80) cc_final: 0.8531 (t80) REVERT: E 40 TYR cc_start: 0.8667 (m-10) cc_final: 0.8047 (m-10) REVERT: E 45 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8537 (tp-100) REVERT: G 22 TYR cc_start: 0.9190 (t80) cc_final: 0.8959 (t80) REVERT: H 45 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8692 (tp-100) REVERT: J 25 LEU cc_start: 0.9455 (mt) cc_final: 0.9226 (mt) REVERT: J 147 SER cc_start: 0.9349 (m) cc_final: 0.9125 (p) REVERT: K 45 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8622 (tp-100) REVERT: K 83 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8375 (mm110) REVERT: L 45 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8630 (tp-100) REVERT: L 143 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8962 (tptt) REVERT: P 83 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8785 (mm-40) REVERT: Q 25 LEU cc_start: 0.9163 (mt) cc_final: 0.8764 (mt) REVERT: Q 29 PHE cc_start: 0.9204 (m-10) cc_final: 0.8972 (m-10) REVERT: Q 83 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8849 (mm-40) REVERT: R 86 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9121 (tppt) REVERT: S 25 LEU cc_start: 0.9036 (mt) cc_final: 0.8782 (mt) REVERT: S 86 LYS cc_start: 0.9236 (ttmm) cc_final: 0.8896 (tppt) REVERT: S 147 SER cc_start: 0.9356 (m) cc_final: 0.9091 (p) REVERT: T 36 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8918 (mm-40) REVERT: T 119 LYS cc_start: 0.9244 (ttpp) cc_final: 0.9031 (mtpp) REVERT: T 143 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8897 (tptt) REVERT: T 152 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8537 (mmt90) REVERT: U 22 TYR cc_start: 0.9132 (t80) cc_final: 0.8740 (t80) REVERT: U 45 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8729 (tp-100) REVERT: V 22 TYR cc_start: 0.8876 (t80) cc_final: 0.8606 (t80) REVERT: V 45 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8506 (tp-100) REVERT: W 22 TYR cc_start: 0.9108 (t80) cc_final: 0.8749 (t80) REVERT: W 147 SER cc_start: 0.9348 (m) cc_final: 0.9068 (p) REVERT: X 22 TYR cc_start: 0.9202 (t80) cc_final: 0.8936 (t80) REVERT: X 45 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8677 (tp-100) REVERT: X 143 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8764 (ttpp) REVERT: Y 22 TYR cc_start: 0.9103 (t80) cc_final: 0.8717 (t80) REVERT: Y 152 ARG cc_start: 0.8346 (mmt90) cc_final: 0.8146 (mmt90) REVERT: Z 45 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8603 (tp-100) outliers start: 153 outliers final: 137 residues processed: 2041 average time/residue: 0.9204 time to fit residues: 3005.6090 Evaluate side-chains 2091 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1952 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 138 LEU Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 148 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 273 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 113 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 32760 Z= 0.364 Angle : 0.669 9.629 44512 Z= 0.373 Chirality : 0.046 0.159 5304 Planarity : 0.004 0.036 5512 Dihedral : 5.480 63.908 4582 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.60 % Allowed : 37.09 % Favored : 58.30 % 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: -1.57 (0.12), residues: 4212 helix: 1.74 (0.13), residues: 1170 sheet: -1.95 (0.14), residues: 1144 loop : -2.27 (0.12), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 92 PHE 0.036 0.002 PHE M 29 TYR 0.028 0.002 TYR E 57 ARG 0.007 0.001 ARG G 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2124 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1966 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9402 (ttpp) cc_final: 0.9003 (mtpp) REVERT: I 143 LYS cc_start: 0.9292 (ttpp) cc_final: 0.8974 (tptt) REVERT: C 45 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8593 (tp-100) REVERT: C 83 GLN cc_start: 0.8898 (mm110) cc_final: 0.8609 (mm110) REVERT: D 36 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8617 (tp40) REVERT: D 40 TYR cc_start: 0.8338 (m-10) cc_final: 0.7972 (m-10) REVERT: E 36 GLN cc_start: 0.9134 (mt0) cc_final: 0.8767 (mm110) REVERT: E 45 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8595 (tp-100) REVERT: G 22 TYR cc_start: 0.9218 (t80) cc_final: 0.9013 (t80) REVERT: H 45 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8771 (tp-100) REVERT: J 25 LEU cc_start: 0.9424 (mt) cc_final: 0.9208 (mt) REVERT: J 36 GLN cc_start: 0.9177 (tt0) cc_final: 0.8854 (tt0) REVERT: J 147 SER cc_start: 0.9367 (m) cc_final: 0.9115 (p) REVERT: K 20 PHE cc_start: 0.8979 (t80) cc_final: 0.8773 (t80) REVERT: K 45 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8617 (tp-100) REVERT: K 83 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8340 (mm110) REVERT: K 86 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8767 (tppt) REVERT: L 20 PHE cc_start: 0.8937 (t80) cc_final: 0.8716 (t80) REVERT: L 45 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8660 (tp-100) REVERT: L 143 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8941 (tptt) REVERT: M 29 PHE cc_start: 0.9141 (m-80) cc_final: 0.8936 (m-80) REVERT: P 83 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8771 (tp40) REVERT: Q 25 LEU cc_start: 0.9183 (mt) cc_final: 0.8803 (mt) REVERT: Q 29 PHE cc_start: 0.9181 (m-10) cc_final: 0.8945 (m-10) REVERT: R 29 PHE cc_start: 0.9138 (m-10) cc_final: 0.8863 (m-10) REVERT: S 25 LEU cc_start: 0.9057 (mt) cc_final: 0.8815 (mt) REVERT: T 36 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8871 (mm-40) REVERT: T 119 LYS cc_start: 0.9263 (ttpp) cc_final: 0.9047 (mtpp) REVERT: T 143 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8857 (tptt) REVERT: T 152 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8528 (mmt90) REVERT: U 22 TYR cc_start: 0.9134 (t80) cc_final: 0.8752 (t80) REVERT: U 40 TYR cc_start: 0.9104 (m-10) cc_final: 0.8879 (m-10) REVERT: V 22 TYR cc_start: 0.8725 (t80) cc_final: 0.8493 (t80) REVERT: V 45 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8498 (tp-100) REVERT: W 119 LYS cc_start: 0.9355 (ttpp) cc_final: 0.9095 (tttp) REVERT: W 147 SER cc_start: 0.9347 (m) cc_final: 0.9142 (p) REVERT: X 22 TYR cc_start: 0.9205 (t80) cc_final: 0.8936 (t80) REVERT: X 45 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8721 (tp-100) REVERT: X 143 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8802 (ttpp) REVERT: Y 22 TYR cc_start: 0.9105 (t80) cc_final: 0.8721 (t80) REVERT: Z 45 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8692 (tp-100) outliers start: 158 outliers final: 149 residues processed: 2020 average time/residue: 0.8722 time to fit residues: 2806.1240 Evaluate side-chains 2087 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1938 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 84 ASP Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain Q residue 147 SER Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 138 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 148 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 350 optimal weight: 0.8980 chunk 373 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 293 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 353 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 49 ASN A 109 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 113 ASN T 113 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.8082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32760 Z= 0.217 Angle : 0.637 9.733 44512 Z= 0.345 Chirality : 0.046 0.170 5304 Planarity : 0.004 0.038 5512 Dihedral : 5.454 77.880 4582 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.64 % Allowed : 38.49 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.12), residues: 4212 helix: 1.96 (0.13), residues: 1170 sheet: -1.84 (0.14), residues: 1144 loop : -2.03 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 92 PHE 0.037 0.002 PHE M 29 TYR 0.027 0.002 TYR F 57 ARG 0.006 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2150 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 2025 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9349 (ttpp) cc_final: 0.8998 (ttmm) REVERT: I 143 LYS cc_start: 0.9130 (ttpp) cc_final: 0.8916 (tptt) REVERT: A 57 TYR cc_start: 0.8609 (m-80) cc_final: 0.8374 (m-80) REVERT: B 86 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8696 (tppt) REVERT: B 147 SER cc_start: 0.9322 (m) cc_final: 0.9058 (p) REVERT: E 36 GLN cc_start: 0.9109 (mt0) cc_final: 0.8704 (mm110) REVERT: E 45 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8343 (tp-100) REVERT: H 45 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8514 (tp-100) REVERT: J 25 LEU cc_start: 0.9318 (mt) cc_final: 0.9105 (mt) REVERT: K 36 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8839 (mm-40) REVERT: K 83 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8194 (mm110) REVERT: K 86 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8533 (tppt) REVERT: K 119 LYS cc_start: 0.9334 (ttpp) cc_final: 0.9110 (tttp) REVERT: L 36 GLN cc_start: 0.9080 (mm110) cc_final: 0.8817 (tp-100) REVERT: L 45 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8515 (tp-100) REVERT: L 72 PHE cc_start: 0.8836 (p90) cc_final: 0.8565 (p90) REVERT: L 143 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8914 (tptt) REVERT: M 72 PHE cc_start: 0.8621 (p90) cc_final: 0.8370 (p90) REVERT: M 83 GLN cc_start: 0.8788 (tp40) cc_final: 0.8469 (mm110) REVERT: N 141 LYS cc_start: 0.9263 (mmtt) cc_final: 0.9003 (mmmm) REVERT: P 83 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8767 (mm110) REVERT: Q 25 LEU cc_start: 0.9083 (mt) cc_final: 0.8726 (mt) REVERT: Q 29 PHE cc_start: 0.9136 (m-10) cc_final: 0.8916 (m-10) REVERT: R 29 PHE cc_start: 0.9079 (m-10) cc_final: 0.8808 (m-10) REVERT: R 86 LYS cc_start: 0.9173 (ttmm) cc_final: 0.8833 (tppt) REVERT: S 76 VAL cc_start: 0.9566 (t) cc_final: 0.9327 (t) REVERT: S 86 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8624 (tppt) REVERT: S 147 SER cc_start: 0.9282 (m) cc_final: 0.8995 (p) REVERT: T 36 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8835 (tp40) REVERT: T 143 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8780 (tptt) REVERT: T 152 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8531 (mmt90) REVERT: U 22 TYR cc_start: 0.9087 (t80) cc_final: 0.8766 (t80) REVERT: U 40 TYR cc_start: 0.9025 (m-10) cc_final: 0.8781 (m-10) REVERT: U 45 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8591 (tp-100) REVERT: V 22 TYR cc_start: 0.8541 (t80) cc_final: 0.8278 (t80) REVERT: V 45 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8264 (tp-100) REVERT: W 22 TYR cc_start: 0.8944 (t80) cc_final: 0.8741 (t80) REVERT: W 36 GLN cc_start: 0.8708 (tt0) cc_final: 0.8457 (tm-30) REVERT: X 22 TYR cc_start: 0.9150 (t80) cc_final: 0.8906 (t80) REVERT: X 57 TYR cc_start: 0.8608 (m-80) cc_final: 0.8400 (m-80) REVERT: X 143 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8661 (ttpp) REVERT: Y 22 TYR cc_start: 0.8979 (t80) cc_final: 0.8569 (t80) REVERT: Y 30 PHE cc_start: 0.9346 (t80) cc_final: 0.9112 (t80) outliers start: 125 outliers final: 108 residues processed: 2056 average time/residue: 0.8583 time to fit residues: 2806.9147 Evaluate side-chains 2073 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1965 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 49 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 148 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 8.9990 chunk 395 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 274 optimal weight: 9.9990 chunk 414 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 ASN T 113 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.8329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32760 Z= 0.222 Angle : 0.653 10.046 44512 Z= 0.353 Chirality : 0.046 0.173 5304 Planarity : 0.004 0.043 5512 Dihedral : 5.460 74.924 4579 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.18 % Allowed : 40.03 % Favored : 56.79 % 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 (0.12), residues: 4212 helix: 2.02 (0.13), residues: 1170 sheet: -1.82 (0.14), residues: 1144 loop : -1.96 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 92 PHE 0.042 0.002 PHE E 30 TYR 0.029 0.002 TYR Z 87 ARG 0.008 0.001 ARG L 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2084 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1975 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9341 (ttpp) cc_final: 0.8967 (ttmm) REVERT: I 143 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8883 (tptt) REVERT: B 147 SER cc_start: 0.9310 (m) cc_final: 0.9062 (p) REVERT: D 30 PHE cc_start: 0.9336 (t80) cc_final: 0.9119 (t80) REVERT: E 36 GLN cc_start: 0.9138 (mt0) cc_final: 0.8735 (mm110) REVERT: E 45 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8242 (tp-100) REVERT: G 36 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9073 (tp40) REVERT: H 45 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8349 (tp-100) REVERT: J 25 LEU cc_start: 0.9306 (mt) cc_final: 0.9099 (mt) REVERT: K 36 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8928 (mm-40) REVERT: K 83 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8273 (mm110) REVERT: K 86 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8393 (tppt) REVERT: K 119 LYS cc_start: 0.9355 (ttpp) cc_final: 0.9136 (tttp) REVERT: L 36 GLN cc_start: 0.9163 (mm110) cc_final: 0.8859 (tp-100) REVERT: L 45 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8488 (tp-100) REVERT: L 143 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8881 (tptt) REVERT: M 83 GLN cc_start: 0.8841 (tp40) cc_final: 0.8511 (mm110) REVERT: P 83 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8763 (mm110) REVERT: Q 22 TYR cc_start: 0.9060 (t80) cc_final: 0.8670 (t80) REVERT: Q 25 LEU cc_start: 0.9069 (mt) cc_final: 0.8716 (mt) REVERT: Q 29 PHE cc_start: 0.9134 (m-10) cc_final: 0.8907 (m-10) REVERT: R 29 PHE cc_start: 0.9062 (m-10) cc_final: 0.8824 (m-10) REVERT: R 86 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8813 (tppt) REVERT: S 86 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8567 (tppt) REVERT: T 36 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8826 (tp-100) REVERT: T 143 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8783 (tptt) REVERT: U 22 TYR cc_start: 0.9065 (t80) cc_final: 0.8762 (t80) REVERT: U 45 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8473 (tp-100) REVERT: V 22 TYR cc_start: 0.8539 (t80) cc_final: 0.8274 (t80) REVERT: V 45 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8226 (tp-100) REVERT: X 22 TYR cc_start: 0.9143 (t80) cc_final: 0.8898 (t80) REVERT: X 143 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8643 (ttpp) REVERT: Y 25 LEU cc_start: 0.9489 (mt) cc_final: 0.9242 (mt) REVERT: Z 36 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8765 (tp-100) REVERT: Z 86 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8437 (tppt) outliers start: 109 outliers final: 98 residues processed: 2007 average time/residue: 0.9283 time to fit residues: 2980.0440 Evaluate side-chains 2044 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1946 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 148 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 0.6980 chunk 351 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 330 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 339 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN E 49 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 49 ASN ** X 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085885 restraints weight = 285577.633| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 5.74 r_work: 0.3343 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32760 Z= 0.214 Angle : 0.653 10.060 44512 Z= 0.351 Chirality : 0.046 0.178 5304 Planarity : 0.004 0.047 5512 Dihedral : 5.436 73.129 4579 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.12 % Allowed : 40.30 % Favored : 56.59 % 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: -1.11 (0.12), residues: 4212 helix: 2.09 (0.13), residues: 1170 sheet: -1.67 (0.14), residues: 1118 loop : -1.97 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 92 PHE 0.040 0.002 PHE E 30 TYR 0.034 0.002 TYR C 57 ARG 0.007 0.001 ARG G 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36044.88 seconds wall clock time: 613 minutes 19.87 seconds (36799.87 seconds total)