Starting phenix.real_space_refine on Thu Sep 26 06:58:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn1_3236/09_2024/5fn1_3236.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.779 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 90 5.49 5 S 108 5.16 5 C 19476 2.51 5 N 5220 2.21 5 O 6336 1.98 5 H 30078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61308 Number of models: 1 Model: "" Number of chains: 2 Chain: "0" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3255 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain: "1" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Classifications: {'RNA': 5} Modifications used: {'3*END': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Restraints were copied for chains: 2, 4, 6, 8, A, C, E, G, I, K, M, O, Q, S, U, W, Y, 3, 5, 7, 9, B, D, F, H, J, L, N, P, R, T, V, X, Z Time building chain proxies: 12.23, per 1000 atoms: 0.20 Number of scatterers: 61308 At special positions: 0 Unit cell: (152.32, 152.32, 133.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 90 15.00 O 6336 8.00 N 5220 7.00 C 19476 6.00 H 30078 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: 13.09 Conformation dependent library (CDL) restraints added in 4.0 seconds 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7308 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 0 sheets defined 50.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 22.72 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 28' Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP C 27 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 28 " --> pdb=" O PRO C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 28' Processing helix chain 'C' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.854A pdb=" N MET C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP C 232 " --> pdb=" O MET C 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP E 27 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE E 28 " --> pdb=" O PRO E 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 28' Processing helix chain 'E' and resid 33 through 41 removed outlier: 3.560A pdb=" N ASP E 39 " --> pdb=" O PRO E 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 89 Processing helix chain 'E' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN E 120 " --> pdb=" O ASP E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 140 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS E 158 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP G 27 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 24 through 28' Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP G 39 " --> pdb=" O PRO G 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN G 120 " --> pdb=" O ASP G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 140 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS G 158 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU G 189 " --> pdb=" O ASN G 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE G 231 " --> pdb=" O THR G 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP G 232 " --> pdb=" O MET G 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP I 27 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE I 28 " --> pdb=" O PRO I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 28' Processing helix chain 'I' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP I 39 " --> pdb=" O PRO I 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE I 58 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 89 Processing helix chain 'I' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN I 120 " --> pdb=" O ASP I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 140 Processing helix chain 'I' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS I 158 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU I 189 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE I 231 " --> pdb=" O THR I 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP K 27 " --> pdb=" O ALA K 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE K 28 " --> pdb=" O PRO K 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 24 through 28' Processing helix chain 'K' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP K 39 " --> pdb=" O PRO K 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE K 58 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN K 120 " --> pdb=" O ASP K 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 117 through 120' Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 140 Processing helix chain 'K' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS K 158 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU K 189 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE K 231 " --> pdb=" O THR K 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP K 232 " --> pdb=" O MET K 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP M 27 " --> pdb=" O ALA M 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE M 28 " --> pdb=" O PRO M 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 28' Processing helix chain 'M' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP M 39 " --> pdb=" O PRO M 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS M 41 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 69 removed outlier: 3.680A pdb=" N ILE M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 60 " --> pdb=" O ALA M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 89 Processing helix chain 'M' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU M 112 " --> pdb=" O SER M 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN M 120 " --> pdb=" O ASP M 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 117 through 120' Processing helix chain 'M' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'M' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS M 158 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU M 189 " --> pdb=" O ASN M 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER M 206 " --> pdb=" O ARG M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 233 removed outlier: 4.173A pdb=" N ILE M 231 " --> pdb=" O THR M 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP M 232 " --> pdb=" O MET M 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE O 28 " --> pdb=" O PRO O 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 24 through 28' Processing helix chain 'O' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP O 39 " --> pdb=" O PRO O 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 89 Processing helix chain 'O' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU O 112 " --> pdb=" O SER O 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE O 116 " --> pdb=" O LEU O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN O 120 " --> pdb=" O ASP O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 117 through 120' Processing helix chain 'O' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 140 Processing helix chain 'O' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS O 158 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU O 189 " --> pdb=" O ASN O 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER O 206 " --> pdb=" O ARG O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE O 231 " --> pdb=" O THR O 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP O 232 " --> pdb=" O MET O 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP Q 27 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE Q 28 " --> pdb=" O PRO Q 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 24 through 28' Processing helix chain 'Q' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP Q 39 " --> pdb=" O PRO Q 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS Q 41 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 60 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 89 Processing helix chain 'Q' and resid 108 through 116 removed outlier: 3.795A pdb=" N LEU Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE Q 116 " --> pdb=" O LEU Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN Q 120 " --> pdb=" O ASP Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 117 through 120' Processing helix chain 'Q' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET Q 128 " --> pdb=" O ARG Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 140 Processing helix chain 'Q' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS Q 158 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU Q 189 " --> pdb=" O ASN Q 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER Q 206 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE Q 231 " --> pdb=" O THR Q 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Q 232 " --> pdb=" O MET Q 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE S 28 " --> pdb=" O PRO S 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 24 through 28' Processing helix chain 'S' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP S 39 " --> pdb=" O PRO S 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS S 41 " --> pdb=" O LEU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE S 58 " --> pdb=" O THR S 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 89 Processing helix chain 'S' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU S 112 " --> pdb=" O SER S 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN S 120 " --> pdb=" O ASP S 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 117 through 120' Processing helix chain 'S' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 140 Processing helix chain 'S' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS S 158 " --> pdb=" O GLU S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU S 189 " --> pdb=" O ASN S 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER S 206 " --> pdb=" O ARG S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE S 231 " --> pdb=" O THR S 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP S 232 " --> pdb=" O MET S 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP U 27 " --> pdb=" O ALA U 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE U 28 " --> pdb=" O PRO U 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 24 through 28' Processing helix chain 'U' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP U 39 " --> pdb=" O PRO U 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS U 41 " --> pdb=" O LEU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 89 Processing helix chain 'U' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU U 112 " --> pdb=" O SER U 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN U 120 " --> pdb=" O ASP U 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 117 through 120' Processing helix chain 'U' and resid 122 through 128 removed outlier: 3.854A pdb=" N MET U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 130 through 140 Processing helix chain 'U' and resid 154 through 158 removed outlier: 3.592A pdb=" N LYS U 158 " --> pdb=" O GLU U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU U 189 " --> pdb=" O ASN U 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER U 206 " --> pdb=" O ARG U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE U 231 " --> pdb=" O THR U 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP U 232 " --> pdb=" O MET U 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP W 27 " --> pdb=" O ALA W 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE W 28 " --> pdb=" O PRO W 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 24 through 28' Processing helix chain 'W' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP W 39 " --> pdb=" O PRO W 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS W 41 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE W 58 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA W 60 " --> pdb=" O ALA W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 89 Processing helix chain 'W' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU W 112 " --> pdb=" O SER W 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE W 116 " --> pdb=" O LEU W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN W 120 " --> pdb=" O ASP W 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 117 through 120' Processing helix chain 'W' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET W 128 " --> pdb=" O ARG W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 140 Processing helix chain 'W' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS W 158 " --> pdb=" O GLU W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU W 189 " --> pdb=" O ASN W 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER W 206 " --> pdb=" O ARG W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE W 231 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP W 232 " --> pdb=" O MET W 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP Y 27 " --> pdb=" O ALA Y 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE Y 28 " --> pdb=" O PRO Y 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 28' Processing helix chain 'Y' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP Y 39 " --> pdb=" O PRO Y 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE Y 58 " --> pdb=" O THR Y 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU Y 112 " --> pdb=" O SER Y 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE Y 116 " --> pdb=" O LEU Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN Y 120 " --> pdb=" O ASP Y 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 117 through 120' Processing helix chain 'Y' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 140 Processing helix chain 'Y' and resid 154 through 158 removed outlier: 3.590A pdb=" N LYS Y 158 " --> pdb=" O GLU Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU Y 189 " --> pdb=" O ASN Y 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER Y 206 " --> pdb=" O ARG Y 202 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE Y 231 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP Y 232 " --> pdb=" O MET Y 228 " (cutoff:3.500A) Processing helix chain '0' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 0 27 " --> pdb=" O ALA 0 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 0 28 " --> pdb=" O PRO 0 25 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 24 through 28' Processing helix chain '0' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 0 39 " --> pdb=" O PRO 0 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 0 41 " --> pdb=" O LEU 0 37 " (cutoff:3.500A) Processing helix chain '0' and resid 54 through 69 removed outlier: 3.680A pdb=" N ILE 0 58 " --> pdb=" O THR 0 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 0 60 " --> pdb=" O ALA 0 56 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 89 Processing helix chain '0' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 0 112 " --> pdb=" O SER 0 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 0 116 " --> pdb=" O LEU 0 112 " (cutoff:3.500A) Processing helix chain '0' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 0 120 " --> pdb=" O ASP 0 117 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 117 through 120' Processing helix chain '0' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 0 128 " --> pdb=" O ARG 0 124 " (cutoff:3.500A) Processing helix chain '0' and resid 130 through 140 Processing helix chain '0' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 0 158 " --> pdb=" O GLU 0 155 " (cutoff:3.500A) Processing helix chain '0' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 0 189 " --> pdb=" O ASN 0 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER 0 206 " --> pdb=" O ARG 0 202 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 0 231 " --> pdb=" O THR 0 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 0 232 " --> pdb=" O MET 0 228 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 2 27 " --> pdb=" O ALA 2 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE 2 28 " --> pdb=" O PRO 2 25 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 24 through 28' Processing helix chain '2' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 2 39 " --> pdb=" O PRO 2 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 2 41 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 2 58 " --> pdb=" O THR 2 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 2 60 " --> pdb=" O ALA 2 56 " (cutoff:3.500A) Processing helix chain '2' and resid 75 through 89 Processing helix chain '2' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 2 112 " --> pdb=" O SER 2 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 2 116 " --> pdb=" O LEU 2 112 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 2 120 " --> pdb=" O ASP 2 117 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 117 through 120' Processing helix chain '2' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 2 128 " --> pdb=" O ARG 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 140 Processing helix chain '2' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 2 158 " --> pdb=" O GLU 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 2 189 " --> pdb=" O ASN 2 185 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER 2 206 " --> pdb=" O ARG 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 2 231 " --> pdb=" O THR 2 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 2 232 " --> pdb=" O MET 2 228 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 28 removed outlier: 3.728A pdb=" N ASP 4 27 " --> pdb=" O ALA 4 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 4 28 " --> pdb=" O PRO 4 25 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 24 through 28' Processing helix chain '4' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 4 39 " --> pdb=" O PRO 4 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 4 41 " --> pdb=" O LEU 4 37 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 4 58 " --> pdb=" O THR 4 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 4 60 " --> pdb=" O ALA 4 56 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 89 Processing helix chain '4' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 4 112 " --> pdb=" O SER 4 108 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE 4 116 " --> pdb=" O LEU 4 112 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN 4 120 " --> pdb=" O ASP 4 117 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 117 through 120' Processing helix chain '4' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 4 128 " --> pdb=" O ARG 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 130 through 140 Processing helix chain '4' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 4 158 " --> pdb=" O GLU 4 155 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 4 189 " --> pdb=" O ASN 4 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 4 206 " --> pdb=" O ARG 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 4 231 " --> pdb=" O THR 4 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 4 232 " --> pdb=" O MET 4 228 " (cutoff:3.500A) Processing helix chain '6' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP 6 27 " --> pdb=" O ALA 6 24 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE 6 28 " --> pdb=" O PRO 6 25 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 24 through 28' Processing helix chain '6' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 6 39 " --> pdb=" O PRO 6 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 6 41 " --> pdb=" O LEU 6 37 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 6 58 " --> pdb=" O THR 6 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 6 60 " --> pdb=" O ALA 6 56 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 89 Processing helix chain '6' and resid 108 through 116 removed outlier: 3.797A pdb=" N LEU 6 112 " --> pdb=" O SER 6 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 6 116 " --> pdb=" O LEU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 120 removed outlier: 3.666A pdb=" N ASN 6 120 " --> pdb=" O ASP 6 117 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 117 through 120' Processing helix chain '6' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 6 128 " --> pdb=" O ARG 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 130 through 140 Processing helix chain '6' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 6 158 " --> pdb=" O GLU 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 185 through 206 removed outlier: 3.541A pdb=" N LEU 6 189 " --> pdb=" O ASN 6 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 6 206 " --> pdb=" O ARG 6 202 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 233 removed outlier: 4.174A pdb=" N ILE 6 231 " --> pdb=" O THR 6 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 6 232 " --> pdb=" O MET 6 228 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 28 removed outlier: 3.729A pdb=" N ASP 8 27 " --> pdb=" O ALA 8 24 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 8 28 " --> pdb=" O PRO 8 25 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 24 through 28' Processing helix chain '8' and resid 33 through 41 removed outlier: 3.561A pdb=" N ASP 8 39 " --> pdb=" O PRO 8 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 8 41 " --> pdb=" O LEU 8 37 " (cutoff:3.500A) Processing helix chain '8' and resid 54 through 69 removed outlier: 3.679A pdb=" N ILE 8 58 " --> pdb=" O THR 8 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 8 60 " --> pdb=" O ALA 8 56 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 89 Processing helix chain '8' and resid 108 through 116 removed outlier: 3.796A pdb=" N LEU 8 112 " --> pdb=" O SER 8 108 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE 8 116 " --> pdb=" O LEU 8 112 " (cutoff:3.500A) Processing helix chain '8' and resid 117 through 120 removed outlier: 3.667A pdb=" N ASN 8 120 " --> pdb=" O ASP 8 117 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 117 through 120' Processing helix chain '8' and resid 122 through 128 removed outlier: 3.855A pdb=" N MET 8 128 " --> pdb=" O ARG 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 130 through 140 Processing helix chain '8' and resid 154 through 158 removed outlier: 3.591A pdb=" N LYS 8 158 " --> pdb=" O GLU 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 185 through 206 removed outlier: 3.540A pdb=" N LEU 8 189 " --> pdb=" O ASN 8 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER 8 206 " --> pdb=" O ARG 8 202 " (cutoff:3.500A) Processing helix chain '8' and resid 227 through 233 removed outlier: 4.173A pdb=" N ILE 8 231 " --> pdb=" O THR 8 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP 8 232 " --> pdb=" O MET 8 228 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2862 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: 19.21 Time building geometry restraints manager: 16.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30060 1.03 - 1.23: 108 1.23 - 1.42: 13068 1.42 - 1.61: 18720 1.61 - 1.80: 198 Bond restraints: 62154 Sorted by residual: bond pdb=" CA PRO Q 234 " pdb=" C PRO Q 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO 2 234 " pdb=" C PRO 2 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO K 234 " pdb=" C PRO K 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO C 234 " pdb=" C PRO C 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.10e+01 bond pdb=" CA PRO U 234 " pdb=" C PRO U 234 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.09e+01 ... (remaining 62149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 96826 2.10 - 4.21: 13121 4.21 - 6.31: 2029 6.31 - 8.42: 488 8.42 - 10.52: 18 Bond angle restraints: 112482 Sorted by residual: angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" C PRO C 234 " ideal model delta sigma weight residual 110.70 117.67 -6.97 1.22e+00 6.72e-01 3.26e+01 angle pdb=" N PRO M 234 " pdb=" CA PRO M 234 " pdb=" C PRO M 234 " ideal model delta sigma weight residual 110.70 117.66 -6.96 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO K 234 " pdb=" CA PRO K 234 " pdb=" C PRO K 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO 0 234 " pdb=" CA PRO 0 234 " pdb=" C PRO 0 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 angle pdb=" N PRO Q 234 " pdb=" CA PRO Q 234 " pdb=" C PRO Q 234 " ideal model delta sigma weight residual 110.70 117.65 -6.95 1.22e+00 6.72e-01 3.25e+01 ... (remaining 112477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 26946 17.24 - 34.49: 1440 34.49 - 51.73: 666 51.73 - 68.98: 864 68.98 - 86.22: 18 Dihedral angle restraints: 29934 sinusoidal: 16866 harmonic: 13068 Sorted by residual: dihedral pdb=" CA TYR E 45 " pdb=" C TYR E 45 " pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR G 45 " pdb=" C TYR G 45 " pdb=" N VAL G 46 " pdb=" CA VAL G 46 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA TYR C 45 " pdb=" C TYR C 45 " pdb=" N VAL C 46 " pdb=" CA VAL C 46 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 29931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3745 0.061 - 0.122: 831 0.122 - 0.184: 334 0.184 - 0.245: 130 0.245 - 0.306: 18 Chirality restraints: 5058 Sorted by residual: chirality pdb=" CA ASN W 209 " pdb=" N ASN W 209 " pdb=" C ASN W 209 " pdb=" CB ASN W 209 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ASN 2 209 " pdb=" N ASN 2 209 " pdb=" C ASN 2 209 " pdb=" CB ASN 2 209 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ASN Y 209 " pdb=" N ASN Y 209 " pdb=" C ASN Y 209 " pdb=" CB ASN Y 209 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 5055 not shown) Planarity restraints: 9090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS 2 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C LYS 2 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS 2 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER 2 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 8 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C LYS 8 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS 8 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER 8 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 93 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C LYS K 93 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS K 93 " -0.010 2.00e-02 2.50e+03 pdb=" N SER K 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 9087 not shown) Histogram of nonbonded interaction distances: 0.26 - 1.13: 670 1.13 - 1.99: 3628 1.99 - 2.86: 151677 2.86 - 3.73: 253911 3.73 - 4.60: 430396 Warning: very small nonbonded interaction distances. Nonbonded interactions: 840282 Sorted by model distance: nonbonded pdb=" O ALA U 72 " pdb=" HB3 SER W 26 " model vdw 0.258 2.620 nonbonded pdb=" O ALA Q 72 " pdb=" HB3 SER S 26 " model vdw 0.258 2.620 nonbonded pdb=" O ALA E 72 " pdb=" HB3 SER G 26 " model vdw 0.259 2.620 nonbonded pdb=" O ALA 4 72 " pdb=" HB3 SER 6 26 " model vdw 0.259 2.620 nonbonded pdb=" O ALA K 72 " pdb=" HB3 SER M 26 " model vdw 0.259 2.620 ... (remaining 840277 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.100 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: 1.910 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 108.510 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.450 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:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3004 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 : 0.009 0.043 32076 Z= 0.553 Angle : 1.180 7.651 44010 Z= 0.771 Chirality : 0.068 0.306 5058 Planarity : 0.005 0.031 5472 Dihedral : 12.984 58.925 12258 Min Nonbonded Distance : 0.877 Molprobity Statistics. All-atom Clashscore : 53.81 Ramachandran Plot: Outliers : 2.79 % Allowed : 8.84 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 3870 helix: -2.67 (0.08), residues: 1692 sheet: None (None), residues: 0 loop : -1.85 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 80 HIS 0.002 0.001 HIS 4 192 PHE 0.010 0.002 PHE O 65 TYR 0.014 0.002 TYR E 210 ARG 0.002 0.000 ARG O 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 3.775 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: C 116 PHE cc_start: 0.7531 (m-80) cc_final: 0.7191 (m-80) REVERT: C 120 ASN cc_start: 0.7718 (m110) cc_final: 0.7514 (m-40) REVERT: E 183 GLN cc_start: 0.7219 (tp-100) cc_final: 0.5853 (pt0) REVERT: E 196 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7362 (tptt) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.9287 time to fit residues: 1005.3855 Evaluate side-chains 507 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN I 120 ASN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 ASN K 209 ASN M 120 ASN M 209 ASN O 120 ASN O 209 ASN Q 120 ASN Q 209 ASN S 115 GLN S 120 ASN S 209 ASN A 120 ASN A 209 ASN ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 209 ASN ** 2 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN 6 209 ASN 8 185 ASN 8 209 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4256 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 32076 Z= 0.448 Angle : 0.893 11.758 44010 Z= 0.482 Chirality : 0.044 0.239 5058 Planarity : 0.007 0.087 5472 Dihedral : 12.775 59.992 5544 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 1.76 % Allowed : 10.08 % Favored : 88.17 % Rotamer: Outliers : 1.87 % Allowed : 7.92 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.14 (0.13), residues: 3870 helix: -1.09 (0.11), residues: 1692 sheet: None (None), residues: 0 loop : -1.69 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP 4 80 HIS 0.010 0.002 HIS W 192 PHE 0.027 0.003 PHE A 164 TYR 0.028 0.003 TYR 6 229 ARG 0.009 0.001 ARG M 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 639 time to evaluate : 3.419 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: C 37 LEU cc_start: 0.7848 (mt) cc_final: 0.7582 (mt) REVERT: C 211 ILE cc_start: 0.6570 (pt) cc_final: 0.6333 (pt) REVERT: E 185 ASN cc_start: 0.8004 (t0) cc_final: 0.7733 (t0) REVERT: E 231 ILE cc_start: 0.5853 (pt) cc_final: 0.5615 (pt) REVERT: O 211 ILE cc_start: 0.6189 (pt) cc_final: 0.5831 (pt) REVERT: Q 126 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5337 (t80) REVERT: A 37 LEU cc_start: 0.7980 (mt) cc_final: 0.7590 (mt) REVERT: 8 61 LEU cc_start: 0.8501 (tp) cc_final: 0.7421 (tp) outliers start: 57 outliers final: 33 residues processed: 679 average time/residue: 0.9250 time to fit residues: 977.7884 Evaluate side-chains 576 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 542 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain U residue 41 LYS Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 51 SER Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain 0 residue 226 ASN Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 226 ASN Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 226 ASN Chi-restraints excluded: chain 4 residue 229 TYR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 209 ASN Chi-restraints excluded: chain 8 residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 285 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN G 147 ASN I 209 ASN ** O 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN W 209 ASN ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 154 GLN ** 8 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4702 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32076 Z= 0.266 Angle : 0.668 8.967 44010 Z= 0.351 Chirality : 0.037 0.236 5058 Planarity : 0.005 0.085 5472 Dihedral : 12.619 62.006 5544 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 1.27 % Allowed : 10.90 % Favored : 87.83 % Rotamer: Outliers : 1.71 % Allowed : 12.20 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.53 (0.13), residues: 3870 helix: -0.27 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.63 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 80 HIS 0.006 0.001 HIS S 221 PHE 0.028 0.002 PHE 6 65 TYR 0.022 0.002 TYR S 45 ARG 0.017 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 678 time to evaluate : 3.494 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: C 37 LEU cc_start: 0.8230 (mt) cc_final: 0.7972 (mt) REVERT: C 175 GLN cc_start: 0.8552 (pm20) cc_final: 0.7850 (pm20) REVERT: E 84 ARG cc_start: 0.7956 (tpt90) cc_final: 0.7612 (tpt90) REVERT: E 88 ASP cc_start: 0.6909 (m-30) cc_final: 0.6520 (m-30) REVERT: E 189 LEU cc_start: 0.8970 (tt) cc_final: 0.8763 (mt) REVERT: I 209 ASN cc_start: 0.5677 (p0) cc_final: 0.5444 (p0) REVERT: Q 139 LEU cc_start: 0.6767 (tt) cc_final: 0.6329 (tt) REVERT: S 61 LEU cc_start: 0.9197 (tp) cc_final: 0.8166 (tp) REVERT: S 65 PHE cc_start: 0.8054 (m-10) cc_final: 0.7627 (m-10) REVERT: A 37 LEU cc_start: 0.8278 (mt) cc_final: 0.7914 (mt) REVERT: A 166 ASP cc_start: 0.8032 (p0) cc_final: 0.7111 (p0) REVERT: U 196 LYS cc_start: 0.8143 (tptt) cc_final: 0.7439 (tttm) REVERT: 4 203 GLN cc_start: 0.6533 (tp40) cc_final: 0.6251 (tp40) REVERT: 6 119 ILE cc_start: 0.7123 (mp) cc_final: 0.6694 (mt) REVERT: 8 61 LEU cc_start: 0.8915 (tp) cc_final: 0.8099 (tp) REVERT: 8 65 PHE cc_start: 0.8344 (m-10) cc_final: 0.8119 (m-10) outliers start: 52 outliers final: 40 residues processed: 709 average time/residue: 0.9007 time to fit residues: 994.6518 Evaluate side-chains 651 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 611 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 229 TYR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 200 LEU Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 229 TYR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain Y residue 51 SER Chi-restraints excluded: chain Y residue 226 ASN Chi-restraints excluded: chain Y residue 229 TYR Chi-restraints excluded: chain 2 residue 66 THR Chi-restraints excluded: chain 2 residue 229 TYR Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 8 residue 50 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 210 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 chunk 180 optimal weight: 0.0060 chunk 327 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 GLN ** M 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.9935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 32076 Z= 0.328 Angle : 0.769 15.031 44010 Z= 0.405 Chirality : 0.041 0.393 5058 Planarity : 0.006 0.090 5472 Dihedral : 12.844 69.700 5544 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 1.27 % Allowed : 10.80 % Favored : 87.93 % Rotamer: Outliers : 2.79 % Allowed : 13.54 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.81 (0.13), residues: 3870 helix: -0.46 (0.12), residues: 1746 sheet: None (None), residues: 0 loop : -1.89 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 148 HIS 0.008 0.002 HIS 6 221 PHE 0.046 0.003 PHE E 162 TYR 0.026 0.002 TYR S 45 ARG 0.047 0.001 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 850 time to evaluate : 3.534 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: C 37 LEU cc_start: 0.8471 (mt) cc_final: 0.8217 (mt) REVERT: C 39 ASP cc_start: 0.7176 (p0) cc_final: 0.6895 (p0) REVERT: C 86 TYR cc_start: 0.9122 (m-80) cc_final: 0.8873 (m-10) REVERT: C 175 GLN cc_start: 0.8628 (pm20) cc_final: 0.8103 (pm20) REVERT: G 163 ASP cc_start: 0.6843 (t0) cc_final: 0.5971 (m-30) REVERT: G 183 GLN cc_start: 0.7841 (tp40) cc_final: 0.6470 (pt0) REVERT: I 58 ILE cc_start: 0.5500 (pt) cc_final: 0.5041 (pt) REVERT: O 75 THR cc_start: 0.5705 (OUTLIER) cc_final: 0.5130 (p) REVERT: O 169 THR cc_start: 0.3217 (OUTLIER) cc_final: 0.2933 (t) REVERT: Q 57 GLU cc_start: 0.7398 (pm20) cc_final: 0.7155 (pm20) REVERT: Q 188 GLU cc_start: 0.6257 (mm-30) cc_final: 0.5996 (mm-30) REVERT: Q 204 LYS cc_start: 0.6848 (tttt) cc_final: 0.6605 (mmtt) REVERT: S 32 ASN cc_start: 0.6226 (OUTLIER) cc_final: 0.5976 (m110) REVERT: S 61 LEU cc_start: 0.9304 (tp) cc_final: 0.8520 (tp) REVERT: S 65 PHE cc_start: 0.8021 (m-10) cc_final: 0.7797 (m-10) REVERT: S 86 TYR cc_start: 0.8947 (m-80) cc_final: 0.8652 (m-10) REVERT: S 121 ILE cc_start: 0.9202 (mm) cc_final: 0.8887 (tt) REVERT: S 204 LYS cc_start: 0.8931 (tptm) cc_final: 0.8643 (tptm) REVERT: A 86 TYR cc_start: 0.9004 (m-80) cc_final: 0.8659 (m-80) REVERT: U 33 THR cc_start: 0.8092 (t) cc_final: 0.7812 (p) REVERT: U 86 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: W 121 ILE cc_start: 0.6960 (mm) cc_final: 0.6508 (mm) REVERT: W 163 ASP cc_start: 0.5231 (m-30) cc_final: 0.4819 (m-30) REVERT: 4 140 ASP cc_start: 0.7326 (p0) cc_final: 0.6566 (t70) REVERT: 6 30 ASN cc_start: 0.4594 (p0) cc_final: 0.4325 (p0) REVERT: 6 91 SER cc_start: 0.7888 (t) cc_final: 0.7010 (p) REVERT: 6 119 ILE cc_start: 0.7649 (mp) cc_final: 0.7169 (mt) REVERT: 6 163 ASP cc_start: 0.7039 (t70) cc_final: 0.6775 (t70) REVERT: 6 203 GLN cc_start: 0.8094 (tp40) cc_final: 0.7852 (tp40) REVERT: 8 30 ASN cc_start: 0.7475 (p0) cc_final: 0.7223 (p0) REVERT: 8 61 LEU cc_start: 0.8944 (tp) cc_final: 0.8647 (tp) REVERT: 8 65 PHE cc_start: 0.8655 (m-10) cc_final: 0.8243 (m-10) REVERT: 8 219 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.6352 (mmt180) REVERT: 8 228 MET cc_start: 0.2846 (ttm) cc_final: 0.2588 (ttm) outliers start: 85 outliers final: 47 residues processed: 901 average time/residue: 0.9016 time to fit residues: 1254.9332 Evaluate side-chains 789 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 738 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 169 THR Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 229 TYR Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain U residue 86 TYR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 141 SER Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 80 TRP Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 154 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 311 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 120 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 ASN A 30 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 GLN Y 154 GLN ** 0 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 142 ASN ** 2 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 115 GLN 8 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 1.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32076 Z= 0.256 Angle : 0.680 9.209 44010 Z= 0.347 Chirality : 0.037 0.175 5058 Planarity : 0.005 0.062 5472 Dihedral : 12.905 71.108 5544 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 1.21 % Allowed : 10.88 % Favored : 87.91 % Rotamer: Outliers : 2.70 % Allowed : 17.88 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.35 (0.14), residues: 3870 helix: 0.10 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.73 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 80 HIS 0.012 0.002 HIS 4 192 PHE 0.027 0.002 PHE K 28 TYR 0.022 0.002 TYR O 129 ARG 0.013 0.001 ARG O 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 884 time to evaluate : 3.489 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: C 121 ILE cc_start: 0.9012 (mm) cc_final: 0.8596 (tt) REVERT: C 165 PHE cc_start: 0.9400 (t80) cc_final: 0.9028 (t80) REVERT: C 175 GLN cc_start: 0.8590 (pm20) cc_final: 0.8033 (pm20) REVERT: C 222 MET cc_start: 0.5949 (ttm) cc_final: 0.5638 (ttm) REVERT: E 33 THR cc_start: 0.7917 (t) cc_final: 0.7654 (p) REVERT: E 50 THR cc_start: 0.9349 (p) cc_final: 0.8849 (t) REVERT: E 122 THR cc_start: 0.9029 (m) cc_final: 0.8795 (p) REVERT: G 163 ASP cc_start: 0.7451 (t0) cc_final: 0.6745 (m-30) REVERT: G 183 GLN cc_start: 0.7929 (tp40) cc_final: 0.6402 (pt0) REVERT: I 90 GLN cc_start: 0.6654 (mp10) cc_final: 0.5000 (mm-40) REVERT: O 70 LEU cc_start: 0.4376 (mm) cc_final: 0.4108 (mm) REVERT: O 182 ARG cc_start: 0.5140 (ptt180) cc_final: 0.3894 (tpt170) REVERT: Q 57 GLU cc_start: 0.7808 (pm20) cc_final: 0.7522 (pm20) REVERT: S 61 LEU cc_start: 0.9288 (tp) cc_final: 0.8685 (tp) REVERT: S 65 PHE cc_start: 0.7699 (m-10) cc_final: 0.7117 (m-10) REVERT: S 121 ILE cc_start: 0.9348 (mm) cc_final: 0.9070 (tt) REVERT: S 163 ASP cc_start: 0.8255 (t0) cc_final: 0.7843 (t0) REVERT: A 32 ASN cc_start: 0.7399 (m-40) cc_final: 0.7195 (m-40) REVERT: A 86 TYR cc_start: 0.9017 (m-80) cc_final: 0.8737 (m-80) REVERT: U 33 THR cc_start: 0.8035 (t) cc_final: 0.7834 (p) REVERT: U 86 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8495 (m-10) REVERT: U 122 THR cc_start: 0.8471 (m) cc_final: 0.8098 (p) REVERT: U 124 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7548 (tpp80) REVERT: U 218 THR cc_start: 0.7642 (p) cc_final: 0.7343 (p) REVERT: W 110 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7773 (ttp-110) REVERT: W 121 ILE cc_start: 0.7183 (mm) cc_final: 0.6794 (mm) REVERT: 0 209 ASN cc_start: 0.7718 (p0) cc_final: 0.7468 (p0) REVERT: 4 128 MET cc_start: 0.6815 (mmm) cc_final: 0.6537 (mmm) REVERT: 4 140 ASP cc_start: 0.7772 (p0) cc_final: 0.7336 (t70) REVERT: 6 30 ASN cc_start: 0.4458 (p0) cc_final: 0.4107 (p0) REVERT: 6 91 SER cc_start: 0.8510 (t) cc_final: 0.7213 (p) REVERT: 6 93 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8164 (mttm) REVERT: 6 119 ILE cc_start: 0.7910 (mp) cc_final: 0.7526 (mt) REVERT: 6 153 TYR cc_start: 0.8417 (m-80) cc_final: 0.8100 (m-80) REVERT: 8 30 ASN cc_start: 0.7837 (p0) cc_final: 0.7602 (p0) REVERT: 8 65 PHE cc_start: 0.8848 (m-10) cc_final: 0.8619 (m-10) REVERT: 8 219 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.6259 (mmt180) outliers start: 82 outliers final: 56 residues processed: 930 average time/residue: 0.8895 time to fit residues: 1280.9292 Evaluate side-chains 877 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 819 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 80 TRP Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 229 TYR Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 86 TYR Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain W residue 228 MET Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 166 ASP Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 4 residue 116 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 4 residue 169 THR Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 228 MET Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 20.0000 chunk 329 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 365 optimal weight: 20.0000 chunk 303 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 192 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 32 ASN E 120 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** U 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** 0 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 154 GLN 6 32 ASN 8 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 1.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32076 Z= 0.197 Angle : 0.618 8.499 44010 Z= 0.313 Chirality : 0.036 0.166 5058 Planarity : 0.005 0.051 5472 Dihedral : 12.813 77.819 5544 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 1.19 % Allowed : 10.54 % Favored : 88.27 % Rotamer: Outliers : 2.43 % Allowed : 20.02 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -1.00 (0.14), residues: 3870 helix: 0.42 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -1.56 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 148 HIS 0.010 0.002 HIS 4 192 PHE 0.022 0.002 PHE K 28 TYR 0.021 0.002 TYR 6 45 ARG 0.007 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 864 time to evaluate : 3.506 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: C 118 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7238 (ttp80) REVERT: C 121 ILE cc_start: 0.9020 (mm) cc_final: 0.8657 (tt) REVERT: C 138 LEU cc_start: 0.9241 (mt) cc_final: 0.9032 (mt) REVERT: C 165 PHE cc_start: 0.9391 (t80) cc_final: 0.9007 (t80) REVERT: C 175 GLN cc_start: 0.8529 (pm20) cc_final: 0.8005 (pm20) REVERT: C 222 MET cc_start: 0.6274 (ttm) cc_final: 0.5732 (ttm) REVERT: E 50 THR cc_start: 0.9392 (p) cc_final: 0.8933 (t) REVERT: E 122 THR cc_start: 0.9014 (m) cc_final: 0.8770 (p) REVERT: G 90 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6889 (mm-40) REVERT: G 122 THR cc_start: 0.7969 (m) cc_final: 0.7290 (p) REVERT: G 163 ASP cc_start: 0.7145 (t0) cc_final: 0.6543 (m-30) REVERT: G 183 GLN cc_start: 0.7813 (tp40) cc_final: 0.6280 (pt0) REVERT: I 90 GLN cc_start: 0.6632 (mp10) cc_final: 0.5468 (mm-40) REVERT: O 159 PHE cc_start: 0.8236 (m-10) cc_final: 0.7988 (m-80) REVERT: O 188 GLU cc_start: 0.5034 (mp0) cc_final: 0.4234 (mp0) REVERT: Q 57 GLU cc_start: 0.7884 (pm20) cc_final: 0.7578 (pm20) REVERT: S 61 LEU cc_start: 0.9273 (tp) cc_final: 0.8597 (tp) REVERT: S 65 PHE cc_start: 0.8024 (m-10) cc_final: 0.7615 (m-10) REVERT: S 103 SER cc_start: 0.8033 (p) cc_final: 0.7822 (t) REVERT: S 121 ILE cc_start: 0.9322 (mm) cc_final: 0.9056 (tt) REVERT: S 163 ASP cc_start: 0.8256 (t0) cc_final: 0.7937 (t0) REVERT: S 170 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 32 ASN cc_start: 0.7022 (m-40) cc_final: 0.6761 (m-40) REVERT: A 86 TYR cc_start: 0.9019 (m-80) cc_final: 0.8724 (m-80) REVERT: U 33 THR cc_start: 0.8094 (t) cc_final: 0.7863 (p) REVERT: U 84 ARG cc_start: 0.8536 (tpt90) cc_final: 0.8296 (tpt90) REVERT: U 86 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: U 122 THR cc_start: 0.8532 (m) cc_final: 0.8213 (p) REVERT: U 218 THR cc_start: 0.7340 (p) cc_final: 0.7084 (p) REVERT: W 159 PHE cc_start: 0.7791 (m-80) cc_final: 0.7580 (m-80) REVERT: W 218 THR cc_start: 0.7020 (p) cc_final: 0.6770 (p) REVERT: Y 90 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.4570 (mm-40) REVERT: 2 128 MET cc_start: 0.3997 (mtp) cc_final: 0.3343 (mtp) REVERT: 4 47 SER cc_start: 0.6606 (p) cc_final: 0.6281 (p) REVERT: 4 65 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6924 (t80) REVERT: 4 79 MET cc_start: 0.7315 (mmp) cc_final: 0.7106 (mmp) REVERT: 4 140 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (t70) REVERT: 4 163 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5931 (t70) REVERT: 4 202 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7310 (ttp-170) REVERT: 6 30 ASN cc_start: 0.4530 (p0) cc_final: 0.4165 (p0) REVERT: 6 91 SER cc_start: 0.8698 (t) cc_final: 0.6954 (p) REVERT: 6 119 ILE cc_start: 0.7951 (mp) cc_final: 0.7574 (mt) REVERT: 6 197 TYR cc_start: 0.7637 (m-80) cc_final: 0.7060 (m-10) REVERT: 8 30 ASN cc_start: 0.7697 (p0) cc_final: 0.7345 (p0) REVERT: 8 182 ARG cc_start: 0.8515 (mtm110) cc_final: 0.8132 (ptm-80) outliers start: 74 outliers final: 60 residues processed: 903 average time/residue: 0.8997 time to fit residues: 1256.3208 Evaluate side-chains 895 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 829 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 ASN Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 86 TYR Chi-restraints excluded: chain U residue 115 GLN Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 229 TYR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 32 ASN Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 2 residue 130 PHE Chi-restraints excluded: chain 4 residue 65 PHE Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 139 LEU Chi-restraints excluded: chain 4 residue 140 ASP Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 6 residue 37 LEU Chi-restraints excluded: chain 6 residue 49 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 228 MET Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 154 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN 2 154 GLN 6 32 ASN 8 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 1.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 32076 Z= 0.375 Angle : 0.843 22.915 44010 Z= 0.449 Chirality : 0.043 0.516 5058 Planarity : 0.007 0.107 5472 Dihedral : 13.822 87.252 5544 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 1.14 % Allowed : 13.62 % Favored : 85.25 % Rotamer: Outliers : 3.58 % Allowed : 20.48 % Favored : 75.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.61 % 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: -1.67 (0.14), residues: 3870 helix: 0.29 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -2.21 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 80 HIS 0.014 0.003 HIS 8 221 PHE 0.034 0.003 PHE 6 165 TYR 0.028 0.003 TYR 0 229 ARG 0.015 0.002 ARG 6 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1118 time to evaluate : 3.527 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: C 88 ASP cc_start: 0.9023 (m-30) cc_final: 0.8768 (t0) REVERT: C 118 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7347 (ttp80) REVERT: C 121 ILE cc_start: 0.9143 (mm) cc_final: 0.8893 (tt) REVERT: C 138 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9223 (mt) REVERT: C 175 GLN cc_start: 0.8772 (pm20) cc_final: 0.8494 (pm20) REVERT: E 50 THR cc_start: 0.9490 (p) cc_final: 0.9225 (t) REVERT: G 74 GLU cc_start: 0.6389 (tm-30) cc_final: 0.6189 (tm-30) REVERT: G 112 LEU cc_start: 0.8862 (mp) cc_final: 0.8472 (mt) REVERT: G 182 ARG cc_start: 0.6600 (tpt170) cc_final: 0.4730 (ttp-170) REVERT: G 183 GLN cc_start: 0.8036 (tp40) cc_final: 0.6736 (pt0) REVERT: G 216 GLU cc_start: 0.7212 (tp30) cc_final: 0.6977 (tp30) REVERT: I 59 GLU cc_start: 0.6088 (tm-30) cc_final: 0.5591 (tm-30) REVERT: I 153 TYR cc_start: 0.8986 (m-80) cc_final: 0.8214 (m-80) REVERT: I 189 LEU cc_start: 0.8906 (tt) cc_final: 0.8675 (tt) REVERT: I 229 TYR cc_start: 0.3319 (OUTLIER) cc_final: 0.2877 (m-10) REVERT: O 178 ASP cc_start: 0.6765 (p0) cc_final: 0.5581 (t0) REVERT: O 188 GLU cc_start: 0.6852 (mp0) cc_final: 0.6378 (mp0) REVERT: Q 79 MET cc_start: 0.8412 (mmp) cc_final: 0.8178 (mmp) REVERT: Q 91 SER cc_start: 0.8987 (t) cc_final: 0.8231 (p) REVERT: Q 129 TYR cc_start: 0.9151 (t80) cc_final: 0.8917 (t80) REVERT: Q 227 THR cc_start: 0.8692 (p) cc_final: 0.8410 (t) REVERT: S 61 LEU cc_start: 0.9307 (tp) cc_final: 0.9056 (tp) REVERT: S 65 PHE cc_start: 0.8476 (m-10) cc_final: 0.8041 (m-10) REVERT: S 203 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8680 (tm-30) REVERT: U 86 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8727 (m-10) REVERT: W 110 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8101 (ttp-110) REVERT: W 216 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6256 (mm-30) REVERT: Y 210 TYR cc_start: 0.7372 (p90) cc_final: 0.7166 (p90) REVERT: 0 121 ILE cc_start: 0.6595 (mm) cc_final: 0.6389 (mm) REVERT: 0 187 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5375 (tptp) REVERT: 0 209 ASN cc_start: 0.8554 (p0) cc_final: 0.8184 (p0) REVERT: 2 79 MET cc_start: 0.7737 (mmp) cc_final: 0.7265 (mmp) REVERT: 4 75 THR cc_start: 0.8066 (m) cc_final: 0.7771 (m) REVERT: 6 30 ASN cc_start: 0.6640 (p0) cc_final: 0.6204 (p0) REVERT: 6 91 SER cc_start: 0.9264 (t) cc_final: 0.8311 (p) REVERT: 6 119 ILE cc_start: 0.8367 (mp) cc_final: 0.8040 (mt) REVERT: 6 154 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7552 (mm110) REVERT: 6 163 ASP cc_start: 0.7321 (t0) cc_final: 0.7018 (t0) REVERT: 8 30 ASN cc_start: 0.7859 (p0) cc_final: 0.7544 (p0) REVERT: 8 33 THR cc_start: 0.8189 (t) cc_final: 0.7926 (t) REVERT: 8 50 THR cc_start: 0.9284 (m) cc_final: 0.9059 (t) REVERT: 8 170 ASN cc_start: 0.8895 (p0) cc_final: 0.8564 (p0) REVERT: 8 175 GLN cc_start: 0.8545 (pp30) cc_final: 0.8201 (pp30) REVERT: 8 219 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.6646 (mtp180) outliers start: 109 outliers final: 75 residues processed: 1168 average time/residue: 0.9015 time to fit residues: 1617.8241 Evaluate side-chains 1096 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1016 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 229 TYR Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 92 SER Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain Q residue 163 ASP Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain U residue 86 TYR Chi-restraints excluded: chain U residue 91 SER Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 110 ARG Chi-restraints excluded: chain W residue 166 ASP Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 236 GLU Chi-restraints excluded: chain 0 residue 187 LYS Chi-restraints excluded: chain 2 residue 68 MET Chi-restraints excluded: chain 2 residue 127 CYS Chi-restraints excluded: chain 2 residue 163 ASP Chi-restraints excluded: chain 4 residue 126 PHE Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 6 residue 32 ASN Chi-restraints excluded: chain 6 residue 108 SER Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 209 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 286 optimal weight: 10.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 120 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN S 32 ASN S 96 GLN S 170 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 ASN W 32 ASN ** 0 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 154 GLN 6 32 ASN ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 1.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 32076 Z= 0.261 Angle : 0.690 9.196 44010 Z= 0.356 Chirality : 0.038 0.162 5058 Planarity : 0.005 0.111 5472 Dihedral : 13.450 77.531 5544 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.52 % Favored : 88.50 % Rotamer: Outliers : 2.73 % Allowed : 24.52 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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 (0.14), residues: 3870 helix: 0.71 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -2.08 (0.14), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 80 HIS 0.009 0.002 HIS O 192 PHE 0.020 0.002 PHE I 162 TYR 0.023 0.002 TYR W 229 ARG 0.015 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1078 time to evaluate : 3.565 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: C 88 ASP cc_start: 0.8951 (m-30) cc_final: 0.8708 (t0) REVERT: C 136 ASN cc_start: 0.9149 (m-40) cc_final: 0.8868 (m-40) REVERT: C 163 ASP cc_start: 0.8245 (t0) cc_final: 0.7842 (t0) REVERT: C 175 GLN cc_start: 0.8595 (pm20) cc_final: 0.8305 (pm20) REVERT: E 50 THR cc_start: 0.9512 (p) cc_final: 0.9269 (t) REVERT: E 84 ARG cc_start: 0.8329 (tpt90) cc_final: 0.8062 (tpt90) REVERT: E 153 TYR cc_start: 0.8981 (m-80) cc_final: 0.8632 (m-80) REVERT: E 163 ASP cc_start: 0.8144 (t0) cc_final: 0.7939 (t0) REVERT: G 182 ARG cc_start: 0.6899 (tpt170) cc_final: 0.5177 (tmm160) REVERT: G 183 GLN cc_start: 0.8050 (tp40) cc_final: 0.6868 (pt0) REVERT: G 216 GLU cc_start: 0.7051 (tp30) cc_final: 0.6816 (tp30) REVERT: I 59 GLU cc_start: 0.6237 (tm-30) cc_final: 0.5623 (tm-30) REVERT: I 153 TYR cc_start: 0.8943 (m-80) cc_final: 0.8386 (m-80) REVERT: I 189 LEU cc_start: 0.8828 (tt) cc_final: 0.8555 (tt) REVERT: K 121 ILE cc_start: 0.7314 (mm) cc_final: 0.7014 (mm) REVERT: M 128 MET cc_start: 0.5289 (ptp) cc_final: 0.4822 (mmm) REVERT: M 187 LYS cc_start: 0.7659 (ttpp) cc_final: 0.7407 (tttt) REVERT: O 156 ASP cc_start: 0.6776 (t0) cc_final: 0.6575 (t0) REVERT: O 178 ASP cc_start: 0.7132 (p0) cc_final: 0.6168 (t0) REVERT: O 188 GLU cc_start: 0.7758 (mp0) cc_final: 0.7464 (mp0) REVERT: Q 108 SER cc_start: 0.7457 (p) cc_final: 0.6792 (p) REVERT: Q 129 TYR cc_start: 0.9085 (t80) cc_final: 0.8871 (t80) REVERT: Q 227 THR cc_start: 0.8797 (p) cc_final: 0.8548 (m) REVERT: S 33 THR cc_start: 0.8029 (t) cc_final: 0.7823 (t) REVERT: S 37 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8152 (mm) REVERT: S 61 LEU cc_start: 0.9274 (tp) cc_final: 0.9052 (tp) REVERT: S 65 PHE cc_start: 0.8491 (m-10) cc_final: 0.8052 (m-10) REVERT: S 103 SER cc_start: 0.8306 (p) cc_final: 0.8102 (t) REVERT: S 203 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8744 (tm-30) REVERT: U 33 THR cc_start: 0.8205 (t) cc_final: 0.7990 (p) REVERT: U 51 SER cc_start: 0.9396 (p) cc_final: 0.9097 (t) REVERT: U 187 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8246 (tptt) REVERT: W 59 GLU cc_start: 0.5813 (tm-30) cc_final: 0.5184 (tm-30) REVERT: W 187 LYS cc_start: 0.8458 (tptt) cc_final: 0.8099 (tppp) REVERT: Y 59 GLU cc_start: 0.5928 (tm-30) cc_final: 0.5716 (tm-30) REVERT: 6 30 ASN cc_start: 0.5756 (p0) cc_final: 0.5430 (p0) REVERT: 6 33 THR cc_start: 0.7722 (t) cc_final: 0.7453 (t) REVERT: 6 41 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6890 (mmtt) REVERT: 6 108 SER cc_start: 0.7985 (p) cc_final: 0.7662 (p) REVERT: 6 118 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7108 (ttm110) REVERT: 6 119 ILE cc_start: 0.8483 (mp) cc_final: 0.8193 (mt) REVERT: 6 165 PHE cc_start: 0.9241 (t80) cc_final: 0.8881 (t80) REVERT: 8 30 ASN cc_start: 0.7695 (p0) cc_final: 0.7298 (p0) REVERT: 8 50 THR cc_start: 0.9313 (m) cc_final: 0.8843 (t) REVERT: 8 84 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7088 (tmm160) REVERT: 8 90 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8451 (mm110) REVERT: 8 170 ASN cc_start: 0.8788 (p0) cc_final: 0.8505 (p0) outliers start: 83 outliers final: 67 residues processed: 1114 average time/residue: 0.9221 time to fit residues: 1583.0357 Evaluate side-chains 1087 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1018 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain M residue 222 MET Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 187 LYS Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 187 LYS Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 226 ASN Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 236 GLU Chi-restraints excluded: chain 0 residue 58 ILE Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 2 residue 236 GLU Chi-restraints excluded: chain 4 residue 140 ASP Chi-restraints excluded: chain 6 residue 137 ILE Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 9.9990 chunk 349 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 348 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN E 32 ASN E 120 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 1.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 32076 Z= 0.320 Angle : 0.741 9.781 44010 Z= 0.385 Chirality : 0.040 0.213 5058 Planarity : 0.006 0.094 5472 Dihedral : 13.738 78.091 5544 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.79 % Favored : 86.28 % Rotamer: Outliers : 3.09 % Allowed : 25.41 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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 (0.14), residues: 3870 helix: 0.67 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP M 80 HIS 0.010 0.003 HIS Q 192 PHE 0.022 0.002 PHE I 162 TYR 0.023 0.002 TYR O 129 ARG 0.010 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1132 time to evaluate : 3.526 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: C 88 ASP cc_start: 0.9026 (m-30) cc_final: 0.8819 (t0) REVERT: C 118 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7304 (ttp80) REVERT: C 163 ASP cc_start: 0.8026 (t0) cc_final: 0.7547 (t0) REVERT: E 84 ARG cc_start: 0.8347 (tpt90) cc_final: 0.8039 (tpt90) REVERT: G 150 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8668 (mtmm) REVERT: G 182 ARG cc_start: 0.6882 (tpt170) cc_final: 0.5207 (tmm160) REVERT: I 59 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5533 (tm-30) REVERT: I 150 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8448 (mmmm) REVERT: I 153 TYR cc_start: 0.8924 (m-80) cc_final: 0.8453 (m-80) REVERT: I 189 LEU cc_start: 0.8930 (tt) cc_final: 0.8597 (tt) REVERT: I 202 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7437 (ttm110) REVERT: K 79 MET cc_start: 0.8490 (mmm) cc_final: 0.7937 (mtt) REVERT: K 222 MET cc_start: 0.6728 (ttm) cc_final: 0.6237 (ttm) REVERT: M 28 PHE cc_start: 0.5115 (t80) cc_final: 0.4608 (t80) REVERT: M 121 ILE cc_start: 0.6119 (mm) cc_final: 0.5781 (mm) REVERT: M 188 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6207 (mt-10) REVERT: O 156 ASP cc_start: 0.7299 (t0) cc_final: 0.7035 (t0) REVERT: O 178 ASP cc_start: 0.7531 (p0) cc_final: 0.6611 (t0) REVERT: O 182 ARG cc_start: 0.8099 (ptt180) cc_final: 0.6687 (tpt170) REVERT: O 187 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: Q 91 SER cc_start: 0.9268 (t) cc_final: 0.8813 (p) REVERT: Q 108 SER cc_start: 0.7531 (p) cc_final: 0.6812 (p) REVERT: Q 129 TYR cc_start: 0.9186 (t80) cc_final: 0.8927 (t80) REVERT: S 65 PHE cc_start: 0.8590 (m-10) cc_final: 0.8291 (m-10) REVERT: S 124 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8497 (tpp80) REVERT: S 163 ASP cc_start: 0.8032 (t0) cc_final: 0.7754 (t0) REVERT: S 203 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8765 (tm-30) REVERT: U 33 THR cc_start: 0.8344 (t) cc_final: 0.8042 (p) REVERT: U 187 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8327 (tptt) REVERT: W 59 GLU cc_start: 0.6019 (tm-30) cc_final: 0.5553 (tm-30) REVERT: W 129 TYR cc_start: 0.8687 (t80) cc_final: 0.8132 (t80) REVERT: Y 97 LEU cc_start: 0.8439 (mp) cc_final: 0.8053 (mp) REVERT: Y 219 ARG cc_start: 0.8596 (ttm110) cc_final: 0.6735 (tpt170) REVERT: 2 79 MET cc_start: 0.7975 (mmp) cc_final: 0.7771 (mmp) REVERT: 4 74 GLU cc_start: 0.6187 (pm20) cc_final: 0.5773 (pm20) REVERT: 4 115 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8168 (mm-40) REVERT: 4 178 ASP cc_start: 0.6450 (m-30) cc_final: 0.6225 (m-30) REVERT: 6 108 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7464 (p) REVERT: 6 119 ILE cc_start: 0.8788 (mp) cc_final: 0.8533 (mt) REVERT: 6 125 GLN cc_start: 0.8977 (mt0) cc_final: 0.8700 (mt0) REVERT: 8 30 ASN cc_start: 0.7929 (p0) cc_final: 0.7490 (p0) REVERT: 8 50 THR cc_start: 0.9339 (m) cc_final: 0.9050 (t) REVERT: 8 84 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7072 (tmm160) REVERT: 8 90 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8482 (mm110) REVERT: 8 108 SER cc_start: 0.8371 (p) cc_final: 0.7974 (p) REVERT: 8 170 ASN cc_start: 0.8778 (p0) cc_final: 0.8523 (p0) outliers start: 94 outliers final: 72 residues processed: 1171 average time/residue: 0.9420 time to fit residues: 1689.4340 Evaluate side-chains 1160 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1085 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 222 MET Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 165 PHE Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 80 TRP Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain O residue 187 LYS Chi-restraints excluded: chain Q residue 188 GLU Chi-restraints excluded: chain Q residue 194 VAL Chi-restraints excluded: chain Q residue 211 ILE Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 187 LYS Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 226 ASN Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 186 GLU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 236 GLU Chi-restraints excluded: chain 2 residue 194 VAL Chi-restraints excluded: chain 2 residue 236 GLU Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 6 residue 108 SER Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 188 GLU Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 ASN E 120 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN Q 203 GLN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 115 GLN 0 203 GLN 2 203 GLN ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 125 GLN 8 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 1.8262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32076 Z= 0.204 Angle : 0.682 10.221 44010 Z= 0.344 Chirality : 0.037 0.174 5058 Planarity : 0.006 0.094 5472 Dihedral : 13.460 79.503 5544 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.61 % Favored : 89.46 % Rotamer: Outliers : 2.30 % Allowed : 27.35 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3870 helix: 0.93 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -1.84 (0.14), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 80 HIS 0.007 0.002 HIS O 192 PHE 0.022 0.002 PHE I 162 TYR 0.016 0.002 TYR S 86 ARG 0.010 0.001 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7740 Ramachandran restraints generated. 3870 Oldfield, 0 Emsley, 3870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1108 time to evaluate : 3.892 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: C 88 ASP cc_start: 0.8862 (m-30) cc_final: 0.8635 (t0) REVERT: C 118 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7254 (ttp80) REVERT: C 136 ASN cc_start: 0.9164 (m-40) cc_final: 0.8853 (m-40) REVERT: C 163 ASP cc_start: 0.7900 (t0) cc_final: 0.7455 (t0) REVERT: G 93 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8623 (mmtp) REVERT: G 150 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8644 (mtmm) REVERT: G 182 ARG cc_start: 0.6763 (tpt170) cc_final: 0.5320 (ptt-90) REVERT: G 228 MET cc_start: 0.2793 (OUTLIER) cc_final: 0.2333 (ttm) REVERT: I 59 GLU cc_start: 0.6007 (tm-30) cc_final: 0.5352 (tm-30) REVERT: I 142 ASN cc_start: 0.8550 (t0) cc_final: 0.8316 (t0) REVERT: I 150 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8280 (mmmm) REVERT: I 153 TYR cc_start: 0.8861 (m-80) cc_final: 0.8452 (m-80) REVERT: I 189 LEU cc_start: 0.8745 (tt) cc_final: 0.8505 (tt) REVERT: I 202 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7549 (ttm110) REVERT: K 79 MET cc_start: 0.8477 (mmm) cc_final: 0.8091 (mtt) REVERT: K 222 MET cc_start: 0.6522 (ttm) cc_final: 0.6081 (ttm) REVERT: M 28 PHE cc_start: 0.4607 (OUTLIER) cc_final: 0.4325 (t80) REVERT: M 121 ILE cc_start: 0.5736 (mm) cc_final: 0.5407 (mm) REVERT: M 170 ASN cc_start: 0.8743 (p0) cc_final: 0.8345 (p0) REVERT: O 156 ASP cc_start: 0.7099 (t0) cc_final: 0.6804 (t0) REVERT: O 178 ASP cc_start: 0.7347 (p0) cc_final: 0.6602 (t0) REVERT: Q 91 SER cc_start: 0.9242 (t) cc_final: 0.8816 (p) REVERT: Q 108 SER cc_start: 0.7475 (p) cc_final: 0.6839 (p) REVERT: Q 129 TYR cc_start: 0.9137 (t80) cc_final: 0.8936 (t80) REVERT: S 163 ASP cc_start: 0.7849 (t0) cc_final: 0.7547 (t0) REVERT: S 203 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 128 MET cc_start: 0.7783 (tpt) cc_final: 0.7487 (tpt) REVERT: U 32 ASN cc_start: 0.7770 (m-40) cc_final: 0.7381 (m-40) REVERT: U 33 THR cc_start: 0.8190 (t) cc_final: 0.7954 (p) REVERT: U 65 PHE cc_start: 0.8536 (m-10) cc_final: 0.8299 (m-10) REVERT: U 187 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8354 (tppt) REVERT: W 59 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5583 (tm-30) REVERT: W 112 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8398 (mt) REVERT: W 129 TYR cc_start: 0.8600 (t80) cc_final: 0.8192 (t80) REVERT: W 136 ASN cc_start: 0.8591 (m-40) cc_final: 0.8316 (m-40) REVERT: W 202 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.8051 (ttp-110) REVERT: Y 97 LEU cc_start: 0.8243 (mp) cc_final: 0.8023 (mp) REVERT: 0 37 LEU cc_start: 0.5096 (pp) cc_final: 0.4208 (tp) REVERT: 2 68 MET cc_start: 0.5902 (tmm) cc_final: 0.5122 (tmm) REVERT: 2 204 LYS cc_start: 0.9141 (tptp) cc_final: 0.8815 (tppt) REVERT: 2 221 HIS cc_start: 0.6738 (m90) cc_final: 0.6491 (m-70) REVERT: 4 204 LYS cc_start: 0.9090 (tptp) cc_final: 0.8871 (tppt) REVERT: 6 28 PHE cc_start: 0.6142 (t80) cc_final: 0.5922 (t80) REVERT: 6 108 SER cc_start: 0.7640 (p) cc_final: 0.7326 (p) REVERT: 6 119 ILE cc_start: 0.8710 (mp) cc_final: 0.8479 (mt) REVERT: 6 124 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8552 (tpp80) REVERT: 6 125 GLN cc_start: 0.8976 (mt0) cc_final: 0.8685 (mt0) REVERT: 8 30 ASN cc_start: 0.7715 (p0) cc_final: 0.7296 (p0) REVERT: 8 50 THR cc_start: 0.9334 (m) cc_final: 0.9020 (t) REVERT: 8 84 ARG cc_start: 0.7960 (tpt170) cc_final: 0.7033 (tmm160) REVERT: 8 90 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8407 (mm110) REVERT: 8 118 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8075 (tpp80) outliers start: 70 outliers final: 54 residues processed: 1135 average time/residue: 0.9126 time to fit residues: 1592.3590 Evaluate side-chains 1134 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1076 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 120 ASN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 203 GLN Chi-restraints excluded: chain M residue 236 GLU Chi-restraints excluded: chain O residue 126 PHE Chi-restraints excluded: chain Q residue 203 GLN Chi-restraints excluded: chain S residue 138 LEU Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 170 ASN Chi-restraints excluded: chain S residue 229 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 187 LYS Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 194 VAL Chi-restraints excluded: chain W residue 236 GLU Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 86 TYR Chi-restraints excluded: chain Y residue 236 GLU Chi-restraints excluded: chain 0 residue 203 GLN Chi-restraints excluded: chain 2 residue 236 GLU Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 6 residue 37 LEU Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 189 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 57 GLU Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 154 GLN Chi-restraints excluded: chain 8 residue 188 GLU Chi-restraints excluded: chain 8 residue 209 ASN Chi-restraints excluded: chain 8 residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 319 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 276 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 300 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 308 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 GLN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 203 GLN ** U 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 203 GLN ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.180001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160600 restraints weight = 147864.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.167103 restraints weight = 64443.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.171074 restraints weight = 33730.719| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 1.8325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.525 32076 Z= 0.454 Angle : 1.020 59.200 44010 Z= 0.621 Chirality : 0.044 1.323 5058 Planarity : 0.006 0.120 5472 Dihedral : 13.461 79.600 5544 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.84 % Favored : 89.25 % Rotamer: Outliers : 2.07 % Allowed : 28.24 % Favored : 69.69 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3870 helix: 0.93 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -1.84 (0.14), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP 0 80 HIS 0.007 0.001 HIS O 192 PHE 0.051 0.002 PHE 4 116 TYR 0.052 0.002 TYR 6 129 ARG 0.026 0.001 ARG Q 84 =============================================================================== Job complete usr+sys time: 18480.54 seconds wall clock time: 313 minutes 56.62 seconds (18836.62 seconds total)