Starting phenix.real_space_refine on Tue Sep 24 08:01:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/09_2024/8rka_19266.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 31872 2.51 5 N 8988 2.21 5 O 9480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50484 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3151 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 26, 'TRANS': 378} Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1056 Classifications: {'peptide': 137} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 130} Restraints were copied for chains: D, F, H, J, L, N, P, R, T, V, X, C, E, G, I, K, M, O, Q, S, U, W Time building chain proxies: 9.43, per 1000 atoms: 0.19 Number of scatterers: 50484 At special positions: 0 Unit cell: (171.722, 171.722, 164.219, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 9480 8.00 N 8988 7.00 C 31872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 4.7 seconds 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12120 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 48 sheets defined 58.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG A 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 19 " --> pdb=" O GLN A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 19' Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.670A pdb=" N ARG A 24 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 30' Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY A 204 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 302 Processing helix chain 'A' and resid 315 through 346 Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 376 through 391 Proline residue: A 385 - end of helix Processing helix chain 'A' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 Processing helix chain 'B' and resid 64 through 79 Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.588A pdb=" N ARG C 18 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 19' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG C 24 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 41 through 54 Processing helix chain 'C' and resid 56 through 71 removed outlier: 4.338A pdb=" N GLN C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.599A pdb=" N ASP C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY C 204 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 Processing helix chain 'C' and resid 315 through 346 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 376 through 391 Proline residue: C 385 - end of helix Processing helix chain 'C' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE D 18 " --> pdb=" O SER D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 87 through 105 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG E 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 19 " --> pdb=" O GLN E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 19' Processing helix chain 'E' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG E 24 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 30' Processing helix chain 'E' and resid 41 through 54 Processing helix chain 'E' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY E 204 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 302 Processing helix chain 'E' and resid 315 through 346 Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'E' and resid 360 through 364 Processing helix chain 'E' and resid 376 through 391 Proline residue: E 385 - end of helix Processing helix chain 'E' and resid 395 through 404 removed outlier: 3.547A pdb=" N VAL E 399 " --> pdb=" O PRO E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE F 18 " --> pdb=" O SER F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 53 Processing helix chain 'F' and resid 64 through 79 Processing helix chain 'F' and resid 87 through 105 Processing helix chain 'G' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG G 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU G 19 " --> pdb=" O GLN G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 19' Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.670A pdb=" N ARG G 24 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 25 through 30' Processing helix chain 'G' and resid 41 through 54 Processing helix chain 'G' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE G 85 " --> pdb=" O ARG G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 127 Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY G 204 " --> pdb=" O ALA G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Proline residue: G 212 - end of helix Processing helix chain 'G' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 302 Processing helix chain 'G' and resid 315 through 346 Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'G' and resid 360 through 364 Processing helix chain 'G' and resid 376 through 391 Proline residue: G 385 - end of helix Processing helix chain 'G' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL G 399 " --> pdb=" O PRO G 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE H 18 " --> pdb=" O SER H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 53 Processing helix chain 'H' and resid 64 through 79 Processing helix chain 'H' and resid 87 through 105 Processing helix chain 'I' and resid 15 through 19 removed outlier: 3.588A pdb=" N ARG I 18 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU I 19 " --> pdb=" O GLN I 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 15 through 19' Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG I 24 " --> pdb=" O GLN I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 25 through 30' Processing helix chain 'I' and resid 41 through 54 Processing helix chain 'I' and resid 56 through 71 removed outlier: 4.338A pdb=" N GLN I 60 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.599A pdb=" N ASP I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY I 204 " --> pdb=" O ALA I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP I 211 " --> pdb=" O ARG I 207 " (cutoff:3.500A) Proline residue: I 212 - end of helix Processing helix chain 'I' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 302 Processing helix chain 'I' and resid 315 through 346 Processing helix chain 'I' and resid 346 through 355 Processing helix chain 'I' and resid 360 through 364 Processing helix chain 'I' and resid 376 through 391 Proline residue: I 385 - end of helix Processing helix chain 'I' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL I 399 " --> pdb=" O PRO I 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE J 18 " --> pdb=" O SER J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 53 Processing helix chain 'J' and resid 64 through 79 Processing helix chain 'J' and resid 87 through 105 Processing helix chain 'K' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG K 18 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU K 19 " --> pdb=" O GLN K 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 15 through 19' Processing helix chain 'K' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG K 24 " --> pdb=" O GLN K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE K 85 " --> pdb=" O ARG K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 127 Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY K 204 " --> pdb=" O ALA K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP K 211 " --> pdb=" O ARG K 207 " (cutoff:3.500A) Proline residue: K 212 - end of helix Processing helix chain 'K' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY K 259 " --> pdb=" O VAL K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 302 Processing helix chain 'K' and resid 315 through 346 Processing helix chain 'K' and resid 346 through 355 Processing helix chain 'K' and resid 360 through 364 Processing helix chain 'K' and resid 376 through 391 Proline residue: K 385 - end of helix Processing helix chain 'K' and resid 395 through 404 removed outlier: 3.547A pdb=" N VAL K 399 " --> pdb=" O PRO K 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE L 18 " --> pdb=" O SER L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 53 Processing helix chain 'L' and resid 64 through 79 Processing helix chain 'L' and resid 87 through 105 Processing helix chain 'M' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG M 18 " --> pdb=" O GLN M 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU M 19 " --> pdb=" O GLN M 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 15 through 19' Processing helix chain 'M' and resid 20 through 24 removed outlier: 3.670A pdb=" N ARG M 24 " --> pdb=" O GLN M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 30' Processing helix chain 'M' and resid 41 through 54 Processing helix chain 'M' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN M 60 " --> pdb=" O ASN M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE M 85 " --> pdb=" O ARG M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 127 Processing helix chain 'M' and resid 128 through 133 Processing helix chain 'M' and resid 157 through 159 No H-bonds generated for 'chain 'M' and resid 157 through 159' Processing helix chain 'M' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY M 204 " --> pdb=" O ALA M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP M 211 " --> pdb=" O ARG M 207 " (cutoff:3.500A) Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY M 259 " --> pdb=" O VAL M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 302 Processing helix chain 'M' and resid 315 through 346 Processing helix chain 'M' and resid 346 through 355 Processing helix chain 'M' and resid 360 through 364 Processing helix chain 'M' and resid 376 through 391 Proline residue: M 385 - end of helix Processing helix chain 'M' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL M 399 " --> pdb=" O PRO M 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 53 Processing helix chain 'N' and resid 64 through 79 Processing helix chain 'N' and resid 87 through 105 Processing helix chain 'O' and resid 15 through 19 removed outlier: 3.588A pdb=" N ARG O 18 " --> pdb=" O GLN O 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU O 19 " --> pdb=" O GLN O 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 15 through 19' Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG O 24 " --> pdb=" O GLN O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA O 29 " --> pdb=" O LEU O 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 25 through 30' Processing helix chain 'O' and resid 41 through 54 Processing helix chain 'O' and resid 56 through 71 removed outlier: 4.338A pdb=" N GLN O 60 " --> pdb=" O ASN O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 116 removed outlier: 3.599A pdb=" N ASP O 115 " --> pdb=" O GLU O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 127 Processing helix chain 'O' and resid 128 through 133 Processing helix chain 'O' and resid 157 through 159 No H-bonds generated for 'chain 'O' and resid 157 through 159' Processing helix chain 'O' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY O 204 " --> pdb=" O ALA O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP O 211 " --> pdb=" O ARG O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY O 259 " --> pdb=" O VAL O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 302 Processing helix chain 'O' and resid 315 through 346 Processing helix chain 'O' and resid 346 through 355 Processing helix chain 'O' and resid 360 through 364 Processing helix chain 'O' and resid 376 through 391 Proline residue: O 385 - end of helix Processing helix chain 'O' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL O 399 " --> pdb=" O PRO O 395 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 14 Processing helix chain 'P' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE P 18 " --> pdb=" O SER P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 53 Processing helix chain 'P' and resid 64 through 79 Processing helix chain 'P' and resid 87 through 105 Processing helix chain 'Q' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG Q 18 " --> pdb=" O GLN Q 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU Q 19 " --> pdb=" O GLN Q 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 15 through 19' Processing helix chain 'Q' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG Q 24 " --> pdb=" O GLN Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 30' Processing helix chain 'Q' and resid 41 through 54 Processing helix chain 'Q' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN Q 60 " --> pdb=" O ASN Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 157 through 159 No H-bonds generated for 'chain 'Q' and resid 157 through 159' Processing helix chain 'Q' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY Q 204 " --> pdb=" O ALA Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP Q 211 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) Proline residue: Q 212 - end of helix Processing helix chain 'Q' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY Q 259 " --> pdb=" O VAL Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 302 Processing helix chain 'Q' and resid 315 through 346 Processing helix chain 'Q' and resid 346 through 355 Processing helix chain 'Q' and resid 360 through 364 Processing helix chain 'Q' and resid 376 through 391 Proline residue: Q 385 - end of helix Processing helix chain 'Q' and resid 395 through 404 removed outlier: 3.547A pdb=" N VAL Q 399 " --> pdb=" O PRO Q 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 14 Processing helix chain 'R' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE R 18 " --> pdb=" O SER R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 53 Processing helix chain 'R' and resid 64 through 79 Processing helix chain 'R' and resid 87 through 105 Processing helix chain 'S' and resid 15 through 19 removed outlier: 3.587A pdb=" N ARG S 18 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU S 19 " --> pdb=" O GLN S 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 15 through 19' Processing helix chain 'S' and resid 20 through 24 removed outlier: 3.670A pdb=" N ARG S 24 " --> pdb=" O GLN S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA S 29 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 25 through 30' Processing helix chain 'S' and resid 41 through 54 Processing helix chain 'S' and resid 56 through 71 removed outlier: 4.339A pdb=" N GLN S 60 " --> pdb=" O ASN S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE S 85 " --> pdb=" O ARG S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 127 Processing helix chain 'S' and resid 128 through 133 Processing helix chain 'S' and resid 157 through 159 No H-bonds generated for 'chain 'S' and resid 157 through 159' Processing helix chain 'S' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY S 204 " --> pdb=" O ALA S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP S 211 " --> pdb=" O ARG S 207 " (cutoff:3.500A) Proline residue: S 212 - end of helix Processing helix chain 'S' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY S 259 " --> pdb=" O VAL S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 282 through 302 Processing helix chain 'S' and resid 315 through 346 Processing helix chain 'S' and resid 346 through 355 Processing helix chain 'S' and resid 360 through 364 Processing helix chain 'S' and resid 376 through 391 Proline residue: S 385 - end of helix Processing helix chain 'S' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL S 399 " --> pdb=" O PRO S 395 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 14 Processing helix chain 'T' and resid 14 through 23 removed outlier: 4.056A pdb=" N ILE T 18 " --> pdb=" O SER T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 53 Processing helix chain 'T' and resid 64 through 79 Processing helix chain 'T' and resid 87 through 105 Processing helix chain 'U' and resid 15 through 19 removed outlier: 3.588A pdb=" N ARG U 18 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU U 19 " --> pdb=" O GLN U 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 15 through 19' Processing helix chain 'U' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG U 24 " --> pdb=" O GLN U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA U 29 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 25 through 30' Processing helix chain 'U' and resid 41 through 54 Processing helix chain 'U' and resid 56 through 71 removed outlier: 4.338A pdb=" N GLN U 60 " --> pdb=" O ASN U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE U 85 " --> pdb=" O ARG U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 116 removed outlier: 3.599A pdb=" N ASP U 115 " --> pdb=" O GLU U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 127 Processing helix chain 'U' and resid 128 through 133 Processing helix chain 'U' and resid 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY U 204 " --> pdb=" O ALA U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 230 removed outlier: 4.821A pdb=" N TRP U 211 " --> pdb=" O ARG U 207 " (cutoff:3.500A) Proline residue: U 212 - end of helix Processing helix chain 'U' and resid 244 through 259 removed outlier: 4.344A pdb=" N GLY U 259 " --> pdb=" O VAL U 255 " (cutoff:3.500A) Processing helix chain 'U' and resid 282 through 302 Processing helix chain 'U' and resid 315 through 346 Processing helix chain 'U' and resid 346 through 355 Processing helix chain 'U' and resid 360 through 364 Processing helix chain 'U' and resid 376 through 391 Proline residue: U 385 - end of helix Processing helix chain 'U' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL U 399 " --> pdb=" O PRO U 395 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 14 Processing helix chain 'V' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE V 18 " --> pdb=" O SER V 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 53 Processing helix chain 'V' and resid 64 through 79 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'W' and resid 15 through 19 removed outlier: 3.588A pdb=" N ARG W 18 " --> pdb=" O GLN W 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU W 19 " --> pdb=" O GLN W 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 15 through 19' Processing helix chain 'W' and resid 20 through 24 removed outlier: 3.671A pdb=" N ARG W 24 " --> pdb=" O GLN W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 30 removed outlier: 4.153A pdb=" N ALA W 29 " --> pdb=" O LEU W 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 25 through 30' Processing helix chain 'W' and resid 41 through 54 Processing helix chain 'W' and resid 56 through 71 removed outlier: 4.338A pdb=" N GLN W 60 " --> pdb=" O ASN W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.635A pdb=" N ILE W 85 " --> pdb=" O ARG W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 116 removed outlier: 3.598A pdb=" N ASP W 115 " --> pdb=" O GLU W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 127 Processing helix chain 'W' and resid 128 through 133 Processing helix chain 'W' and resid 157 through 159 No H-bonds generated for 'chain 'W' and resid 157 through 159' Processing helix chain 'W' and resid 200 through 204 removed outlier: 4.238A pdb=" N GLY W 204 " --> pdb=" O ALA W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 205 through 230 removed outlier: 4.820A pdb=" N TRP W 211 " --> pdb=" O ARG W 207 " (cutoff:3.500A) Proline residue: W 212 - end of helix Processing helix chain 'W' and resid 244 through 259 removed outlier: 4.343A pdb=" N GLY W 259 " --> pdb=" O VAL W 255 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 302 Processing helix chain 'W' and resid 315 through 346 Processing helix chain 'W' and resid 346 through 355 Processing helix chain 'W' and resid 360 through 364 Processing helix chain 'W' and resid 376 through 391 Proline residue: W 385 - end of helix Processing helix chain 'W' and resid 395 through 404 removed outlier: 3.548A pdb=" N VAL W 399 " --> pdb=" O PRO W 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 14 Processing helix chain 'X' and resid 14 through 23 removed outlier: 4.055A pdb=" N ILE X 18 " --> pdb=" O SER X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 53 Processing helix chain 'X' and resid 64 through 79 Processing helix chain 'X' and resid 87 through 105 Processing sheet with id=1, first strand: chain 'A' and resid 90 through 93 Processing sheet with id=2, first strand: chain 'A' and resid 148 through 156 removed outlier: 6.784A pdb=" N GLU A 140 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 153 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 138 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS A 155 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS A 136 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU A 170 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=5, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=6, first strand: chain 'C' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU C 140 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE C 153 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU C 138 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N HIS C 155 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS C 136 " --> pdb=" O HIS C 155 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU C 170 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=9, first strand: chain 'E' and resid 90 through 93 Processing sheet with id=10, first strand: chain 'E' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU E 140 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE E 153 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU E 138 " --> pdb=" O PHE E 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS E 155 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS E 136 " --> pdb=" O HIS E 155 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU E 170 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=13, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=14, first strand: chain 'G' and resid 148 through 156 removed outlier: 6.784A pdb=" N GLU G 140 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE G 153 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU G 138 " --> pdb=" O PHE G 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS G 155 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS G 136 " --> pdb=" O HIS G 155 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'G' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU G 170 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=17, first strand: chain 'I' and resid 90 through 93 Processing sheet with id=18, first strand: chain 'I' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU I 140 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE I 153 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU I 138 " --> pdb=" O PHE I 153 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N HIS I 155 " --> pdb=" O CYS I 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS I 136 " --> pdb=" O HIS I 155 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU I 170 " --> pdb=" O ASN I 164 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'I' and resid 235 through 238 Processing sheet with id=21, first strand: chain 'K' and resid 90 through 93 Processing sheet with id=22, first strand: chain 'K' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU K 140 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE K 153 " --> pdb=" O GLU K 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU K 138 " --> pdb=" O PHE K 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS K 155 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS K 136 " --> pdb=" O HIS K 155 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'K' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU K 170 " --> pdb=" O ASN K 164 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'K' and resid 235 through 238 Processing sheet with id=25, first strand: chain 'M' and resid 90 through 93 Processing sheet with id=26, first strand: chain 'M' and resid 148 through 156 removed outlier: 6.784A pdb=" N GLU M 140 " --> pdb=" O LEU M 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE M 153 " --> pdb=" O GLU M 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU M 138 " --> pdb=" O PHE M 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS M 155 " --> pdb=" O CYS M 136 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS M 136 " --> pdb=" O HIS M 155 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'M' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU M 170 " --> pdb=" O ASN M 164 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'M' and resid 235 through 238 Processing sheet with id=29, first strand: chain 'O' and resid 90 through 93 Processing sheet with id=30, first strand: chain 'O' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU O 140 " --> pdb=" O LEU O 151 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE O 153 " --> pdb=" O GLU O 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU O 138 " --> pdb=" O PHE O 153 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N HIS O 155 " --> pdb=" O CYS O 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS O 136 " --> pdb=" O HIS O 155 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'O' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU O 170 " --> pdb=" O ASN O 164 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'O' and resid 235 through 238 Processing sheet with id=33, first strand: chain 'Q' and resid 90 through 93 Processing sheet with id=34, first strand: chain 'Q' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU Q 140 " --> pdb=" O LEU Q 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE Q 153 " --> pdb=" O GLU Q 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU Q 138 " --> pdb=" O PHE Q 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS Q 155 " --> pdb=" O CYS Q 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS Q 136 " --> pdb=" O HIS Q 155 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'Q' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU Q 170 " --> pdb=" O ASN Q 164 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'Q' and resid 235 through 238 Processing sheet with id=37, first strand: chain 'S' and resid 90 through 93 Processing sheet with id=38, first strand: chain 'S' and resid 148 through 156 removed outlier: 6.784A pdb=" N GLU S 140 " --> pdb=" O LEU S 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE S 153 " --> pdb=" O GLU S 138 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU S 138 " --> pdb=" O PHE S 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS S 155 " --> pdb=" O CYS S 136 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS S 136 " --> pdb=" O HIS S 155 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU S 170 " --> pdb=" O ASN S 164 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 235 through 238 Processing sheet with id=41, first strand: chain 'U' and resid 90 through 93 Processing sheet with id=42, first strand: chain 'U' and resid 148 through 156 removed outlier: 6.785A pdb=" N GLU U 140 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE U 153 " --> pdb=" O GLU U 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU U 138 " --> pdb=" O PHE U 153 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N HIS U 155 " --> pdb=" O CYS U 136 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS U 136 " --> pdb=" O HIS U 155 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU U 170 " --> pdb=" O ASN U 164 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'U' and resid 235 through 238 Processing sheet with id=45, first strand: chain 'W' and resid 90 through 93 Processing sheet with id=46, first strand: chain 'W' and resid 148 through 156 removed outlier: 6.784A pdb=" N GLU W 140 " --> pdb=" O LEU W 151 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE W 153 " --> pdb=" O GLU W 138 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU W 138 " --> pdb=" O PHE W 153 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N HIS W 155 " --> pdb=" O CYS W 136 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N CYS W 136 " --> pdb=" O HIS W 155 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'W' and resid 161 through 164 removed outlier: 6.002A pdb=" N GLU W 170 " --> pdb=" O ASN W 164 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'W' and resid 235 through 238 2724 hydrogen bonds defined for protein. 7884 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: 14.36 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 17304 1.34 - 1.46: 9169 1.46 - 1.58: 24851 1.58 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 51576 Sorted by residual: bond pdb=" N ALA E 278 " pdb=" CA ALA E 278 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.20e-02 6.94e+03 8.37e-01 bond pdb=" N ALA K 278 " pdb=" CA ALA K 278 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.20e-02 6.94e+03 8.37e-01 bond pdb=" N ALA Q 278 " pdb=" CA ALA Q 278 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.20e-02 6.94e+03 8.37e-01 bond pdb=" N ALA A 278 " pdb=" CA ALA A 278 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.20e-02 6.94e+03 8.25e-01 bond pdb=" N ALA G 278 " pdb=" CA ALA G 278 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.20e-02 6.94e+03 8.25e-01 ... (remaining 51571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 66723 0.91 - 1.83: 2502 1.83 - 2.74: 495 2.74 - 3.66: 304 3.66 - 4.57: 104 Bond angle restraints: 70128 Sorted by residual: angle pdb=" N ALA I 277 " pdb=" CA ALA I 277 " pdb=" C ALA I 277 " ideal model delta sigma weight residual 111.02 113.34 -2.32 1.22e+00 6.72e-01 3.63e+00 angle pdb=" N ALA O 277 " pdb=" CA ALA O 277 " pdb=" C ALA O 277 " ideal model delta sigma weight residual 111.02 113.34 -2.32 1.22e+00 6.72e-01 3.63e+00 angle pdb=" N ALA C 277 " pdb=" CA ALA C 277 " pdb=" C ALA C 277 " ideal model delta sigma weight residual 111.02 113.34 -2.32 1.22e+00 6.72e-01 3.63e+00 angle pdb=" N ALA U 277 " pdb=" CA ALA U 277 " pdb=" C ALA U 277 " ideal model delta sigma weight residual 111.02 113.34 -2.32 1.22e+00 6.72e-01 3.63e+00 angle pdb=" N ALA M 277 " pdb=" CA ALA M 277 " pdb=" C ALA M 277 " ideal model delta sigma weight residual 111.02 113.34 -2.32 1.22e+00 6.72e-01 3.62e+00 ... (remaining 70123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 28604 17.69 - 35.38: 2161 35.38 - 53.07: 303 53.07 - 70.77: 108 70.77 - 88.46: 72 Dihedral angle restraints: 31248 sinusoidal: 12480 harmonic: 18768 Sorted by residual: dihedral pdb=" CA PHE E 274 " pdb=" C PHE E 274 " pdb=" N GLN E 275 " pdb=" CA GLN E 275 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE K 274 " pdb=" C PHE K 274 " pdb=" N GLN K 275 " pdb=" CA GLN K 275 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE Q 274 " pdb=" C PHE Q 274 " pdb=" N GLN Q 275 " pdb=" CA GLN Q 275 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 31245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4902 0.027 - 0.055: 2054 0.055 - 0.082: 548 0.082 - 0.109: 184 0.109 - 0.136: 112 Chirality restraints: 7800 Sorted by residual: chirality pdb=" CA ILE K 394 " pdb=" N ILE K 394 " pdb=" C ILE K 394 " pdb=" CB ILE K 394 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE Q 394 " pdb=" N ILE Q 394 " pdb=" C ILE Q 394 " pdb=" CB ILE Q 394 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE M 394 " pdb=" N ILE M 394 " pdb=" C ILE M 394 " pdb=" CB ILE M 394 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 7797 not shown) Planarity restraints: 9252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 119 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO X 120 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO X 120 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO X 120 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 119 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO D 120 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 120 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 120 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA V 119 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO V 120 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO V 120 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO V 120 " 0.036 5.00e-02 4.00e+02 ... (remaining 9249 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 864 2.65 - 3.22: 47644 3.22 - 3.78: 77634 3.78 - 4.34: 104567 4.34 - 4.90: 176876 Nonbonded interactions: 407585 Sorted by model distance: nonbonded pdb=" O TYR D 13 " pdb=" OG SER D 14 " model vdw 2.094 3.040 nonbonded pdb=" O TYR J 13 " pdb=" OG SER J 14 " model vdw 2.094 3.040 nonbonded pdb=" O TYR P 13 " pdb=" OG SER P 14 " model vdw 2.094 3.040 nonbonded pdb=" O TYR V 13 " pdb=" OG SER V 14 " model vdw 2.094 3.040 nonbonded pdb=" O TYR T 13 " pdb=" OG SER T 14 " model vdw 2.094 3.040 ... (remaining 407580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 68.490 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.002 0.022 51576 Z= 0.160 Angle : 0.488 4.570 70128 Z= 0.251 Chirality : 0.036 0.136 7800 Planarity : 0.004 0.066 9252 Dihedral : 13.373 88.458 19128 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.11), residues: 6456 helix: 2.78 (0.09), residues: 3192 sheet: 0.91 (0.24), residues: 552 loop : 0.35 (0.12), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 188 HIS 0.004 0.001 HIS Q 110 PHE 0.015 0.001 PHE S 274 TYR 0.022 0.001 TYR W 230 ARG 0.003 0.000 ARG W 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1316 time to evaluate : 4.098 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: D 27 LYS cc_start: 0.5706 (tptp) cc_final: 0.5484 (mttm) REVERT: D 72 CYS cc_start: 0.7272 (m) cc_final: 0.6836 (m) REVERT: F 27 LYS cc_start: 0.5546 (tptp) cc_final: 0.5274 (mttt) REVERT: F 72 CYS cc_start: 0.7050 (m) cc_final: 0.6821 (m) REVERT: H 27 LYS cc_start: 0.5716 (tptp) cc_final: 0.5169 (mttt) REVERT: I 377 ILE cc_start: 0.7144 (mp) cc_final: 0.6873 (pt) REVERT: J 27 LYS cc_start: 0.6399 (tptp) cc_final: 0.5385 (mttp) REVERT: K 362 ARG cc_start: 0.6089 (tpt170) cc_final: 0.5823 (mmm160) REVERT: L 27 LYS cc_start: 0.6755 (tptp) cc_final: 0.5465 (mttp) REVERT: M 144 GLN cc_start: 0.6555 (mp10) cc_final: 0.6053 (mt0) REVERT: M 362 ARG cc_start: 0.6357 (tpt170) cc_final: 0.5950 (mmm160) REVERT: N 27 LYS cc_start: 0.6602 (tptp) cc_final: 0.5180 (mttm) REVERT: O 144 GLN cc_start: 0.6780 (mp10) cc_final: 0.6301 (mt0) REVERT: O 362 ARG cc_start: 0.6518 (tpt170) cc_final: 0.6072 (mmm160) REVERT: R 128 SER cc_start: 0.8451 (m) cc_final: 0.8041 (t) REVERT: T 20 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6490 (mt-10) REVERT: T 132 ASN cc_start: 0.8021 (t0) cc_final: 0.7700 (t0) REVERT: U 85 ILE cc_start: 0.8437 (mt) cc_final: 0.8188 (mt) REVERT: V 20 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6805 (mt-10) REVERT: V 132 ASN cc_start: 0.7423 (t0) cc_final: 0.7023 (t0) REVERT: X 20 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6557 (mt-10) outliers start: 0 outliers final: 0 residues processed: 1316 average time/residue: 0.5670 time to fit residues: 1181.7743 Evaluate side-chains 731 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 0.5980 chunk 482 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 chunk 498 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 303 optimal weight: 0.5980 chunk 371 optimal weight: 5.9990 chunk 577 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS C 164 ASN D 53 HIS D 126 GLN E 164 ASN F 53 HIS H 53 HIS I 191 HIS ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS K 110 HIS K 191 HIS L 26 ASN L 53 HIS P 26 ASN P 126 GLN ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 GLN T 126 GLN V 126 GLN W 97 ASN X 53 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51576 Z= 0.225 Angle : 0.622 9.477 70128 Z= 0.317 Chirality : 0.042 0.261 7800 Planarity : 0.005 0.062 9252 Dihedral : 3.983 21.881 7080 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.06 % Allowed : 8.89 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.10), residues: 6456 helix: 2.55 (0.09), residues: 3216 sheet: 1.45 (0.24), residues: 456 loop : 0.41 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 188 HIS 0.004 0.001 HIS S 260 PHE 0.013 0.001 PHE S 285 TYR 0.026 0.002 TYR A 230 ARG 0.010 0.001 ARG M 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 836 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8095 (mp) REVERT: D 27 LYS cc_start: 0.6373 (tptp) cc_final: 0.5870 (mttm) REVERT: E 18 ARG cc_start: 0.6886 (mmt90) cc_final: 0.6653 (tpp-160) REVERT: E 56 ASN cc_start: 0.6410 (t0) cc_final: 0.6209 (t0) REVERT: F 27 LYS cc_start: 0.6160 (tptp) cc_final: 0.5645 (mttt) REVERT: F 49 ASP cc_start: 0.6926 (m-30) cc_final: 0.6550 (m-30) REVERT: G 149 MET cc_start: 0.5708 (mmm) cc_final: 0.5231 (mmm) REVERT: G 377 ILE cc_start: 0.6839 (mp) cc_final: 0.6575 (tt) REVERT: H 27 LYS cc_start: 0.6351 (tptp) cc_final: 0.5478 (mttt) REVERT: H 49 ASP cc_start: 0.6890 (m-30) cc_final: 0.6577 (m-30) REVERT: I 377 ILE cc_start: 0.7052 (mp) cc_final: 0.6785 (pt) REVERT: J 27 LYS cc_start: 0.6831 (tptp) cc_final: 0.5626 (mttm) REVERT: J 45 ASP cc_start: 0.8079 (m-30) cc_final: 0.7840 (m-30) REVERT: J 51 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7152 (t-90) REVERT: J 115 ASP cc_start: 0.3951 (p0) cc_final: 0.3724 (p0) REVERT: K 65 MET cc_start: 0.8186 (mtt) cc_final: 0.7690 (mtt) REVERT: K 273 ASP cc_start: 0.6752 (p0) cc_final: 0.6366 (p0) REVERT: L 27 LYS cc_start: 0.7056 (tptp) cc_final: 0.5786 (mttm) REVERT: L 38 ASP cc_start: 0.8469 (m-30) cc_final: 0.8251 (m-30) REVERT: M 144 GLN cc_start: 0.6621 (mp10) cc_final: 0.6242 (mt0) REVERT: N 27 LYS cc_start: 0.6915 (tptp) cc_final: 0.5412 (mttm) REVERT: N 46 SER cc_start: 0.8735 (m) cc_final: 0.8520 (m) REVERT: O 96 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6282 (ttp-110) REVERT: O 144 GLN cc_start: 0.6866 (mp10) cc_final: 0.6458 (mt0) REVERT: T 132 ASN cc_start: 0.8374 (t0) cc_final: 0.7984 (t0) REVERT: U 380 MET cc_start: 0.7317 (mmm) cc_final: 0.6660 (mmm) REVERT: V 20 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6880 (mt-10) REVERT: V 132 ASN cc_start: 0.7628 (t0) cc_final: 0.7350 (t0) REVERT: W 294 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7080 (t0) REVERT: X 126 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.5803 (mp10) outliers start: 108 outliers final: 60 residues processed: 903 average time/residue: 0.5247 time to fit residues: 773.6646 Evaluate side-chains 727 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 662 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 51 HIS Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 351 LEU Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 96 ARG Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 96 ARG Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 368 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 245 ASP Chi-restraints excluded: chain U residue 376 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 294 ASP Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 126 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 480 optimal weight: 0.6980 chunk 393 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 578 optimal weight: 3.9990 chunk 625 optimal weight: 0.9980 chunk 515 optimal weight: 0.0370 chunk 573 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 464 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN C 164 ASN C 184 GLN C 276 GLN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN I 276 GLN I 337 GLN J 12 GLN J 26 ASN K 337 GLN M 110 HIS M 337 GLN N 126 GLN R 78 ASN W 97 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 51576 Z= 0.211 Angle : 0.567 7.534 70128 Z= 0.289 Chirality : 0.040 0.256 7800 Planarity : 0.005 0.062 9252 Dihedral : 3.905 31.480 7080 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 1.97 % Allowed : 10.68 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.38 (0.11), residues: 6456 helix: 2.67 (0.09), residues: 3216 sheet: 1.35 (0.24), residues: 456 loop : 0.36 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 398 HIS 0.008 0.001 HIS A 323 PHE 0.023 0.001 PHE K 206 TYR 0.016 0.001 TYR A 230 ARG 0.017 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 751 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.7259 (mmp) cc_final: 0.6808 (mmm) REVERT: B 16 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 49 ASP cc_start: 0.7539 (m-30) cc_final: 0.7087 (m-30) REVERT: B 74 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8711 (mp) REVERT: D 47 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: E 149 MET cc_start: 0.6298 (mmm) cc_final: 0.6058 (mmm) REVERT: F 27 LYS cc_start: 0.6823 (tptp) cc_final: 0.5922 (mttm) REVERT: F 49 ASP cc_start: 0.7478 (m-30) cc_final: 0.7168 (m-30) REVERT: G 149 MET cc_start: 0.6280 (mmm) cc_final: 0.5658 (mmm) REVERT: G 229 ILE cc_start: 0.8569 (tp) cc_final: 0.8240 (tp) REVERT: G 377 ILE cc_start: 0.7019 (mp) cc_final: 0.6748 (pt) REVERT: H 27 LYS cc_start: 0.6674 (tptp) cc_final: 0.5541 (mttt) REVERT: H 38 ASP cc_start: 0.8196 (m-30) cc_final: 0.7950 (m-30) REVERT: H 49 ASP cc_start: 0.7281 (m-30) cc_final: 0.6926 (m-30) REVERT: I 377 ILE cc_start: 0.7140 (mp) cc_final: 0.6832 (pt) REVERT: J 23 ASP cc_start: 0.6578 (t70) cc_final: 0.5883 (t70) REVERT: J 27 LYS cc_start: 0.7185 (tptp) cc_final: 0.5888 (mttm) REVERT: J 45 ASP cc_start: 0.8338 (m-30) cc_final: 0.7854 (m-30) REVERT: K 288 MET cc_start: 0.8676 (tpp) cc_final: 0.7716 (tpt) REVERT: L 27 LYS cc_start: 0.7162 (tptp) cc_final: 0.5904 (mttp) REVERT: M 144 GLN cc_start: 0.6664 (mp10) cc_final: 0.6452 (mt0) REVERT: N 46 SER cc_start: 0.8845 (m) cc_final: 0.8580 (m) REVERT: Q 288 MET cc_start: 0.8813 (tpp) cc_final: 0.8284 (tpt) REVERT: T 132 ASN cc_start: 0.8512 (t0) cc_final: 0.8166 (t0) REVERT: U 77 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: U 114 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7859 (tt) REVERT: V 47 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: V 78 ASN cc_start: 0.8153 (m-40) cc_final: 0.7898 (m-40) REVERT: V 132 ASN cc_start: 0.7914 (t0) cc_final: 0.7696 (t0) REVERT: W 47 ARG cc_start: 0.6729 (ttm170) cc_final: 0.6528 (mtp180) REVERT: W 114 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8026 (tt) outliers start: 103 outliers final: 62 residues processed: 823 average time/residue: 0.5185 time to fit residues: 701.1331 Evaluate side-chains 714 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 646 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 230 TYR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 230 TYR Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 376 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 0.0040 chunk 435 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 388 optimal weight: 0.1980 chunk 580 optimal weight: 4.9990 chunk 614 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 550 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 337 GLN E 184 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 HIS L 26 ASN O 337 GLN W 97 ASN W 164 ASN W 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51576 Z= 0.230 Angle : 0.596 7.483 70128 Z= 0.304 Chirality : 0.041 0.162 7800 Planarity : 0.005 0.056 9252 Dihedral : 4.122 28.637 7080 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.99 % Rotamer: Outliers : 2.81 % Allowed : 11.75 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.11), residues: 6456 helix: 2.52 (0.09), residues: 3228 sheet: 1.11 (0.24), residues: 456 loop : 0.19 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 348 HIS 0.006 0.001 HIS K 217 PHE 0.018 0.001 PHE G 186 TYR 0.015 0.001 TYR C 230 ARG 0.012 0.001 ARG E 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 715 time to evaluate : 4.214 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: A 380 MET cc_start: 0.7658 (mmp) cc_final: 0.7338 (mmm) REVERT: B 16 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 74 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8910 (mp) REVERT: E 149 MET cc_start: 0.6616 (mmm) cc_final: 0.6028 (mmm) REVERT: F 27 LYS cc_start: 0.7261 (tptp) cc_final: 0.6028 (mttp) REVERT: G 229 ILE cc_start: 0.8609 (tp) cc_final: 0.8242 (tp) REVERT: G 250 THR cc_start: 0.9119 (m) cc_final: 0.8856 (m) REVERT: G 377 ILE cc_start: 0.7132 (mp) cc_final: 0.6846 (pt) REVERT: H 12 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7428 (tt0) REVERT: H 27 LYS cc_start: 0.7252 (tptp) cc_final: 0.5944 (mttm) REVERT: H 38 ASP cc_start: 0.8338 (m-30) cc_final: 0.8130 (m-30) REVERT: H 49 ASP cc_start: 0.7692 (m-30) cc_final: 0.7277 (m-30) REVERT: I 377 ILE cc_start: 0.7220 (mp) cc_final: 0.6951 (pt) REVERT: J 12 GLN cc_start: 0.7702 (tp40) cc_final: 0.7480 (tt0) REVERT: L 5 THR cc_start: 0.8293 (p) cc_final: 0.8078 (p) REVERT: L 27 LYS cc_start: 0.7320 (tptp) cc_final: 0.6033 (mttp) REVERT: M 288 MET cc_start: 0.8896 (tpp) cc_final: 0.8448 (tpt) REVERT: Q 288 MET cc_start: 0.8841 (tpp) cc_final: 0.8457 (tpt) REVERT: Q 368 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (m) REVERT: S 229 ILE cc_start: 0.8319 (tp) cc_final: 0.8107 (tp) REVERT: T 132 ASN cc_start: 0.8572 (t0) cc_final: 0.8261 (t0) REVERT: U 114 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8101 (tt) REVERT: V 16 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7611 (tt0) REVERT: V 47 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: V 132 ASN cc_start: 0.8254 (t0) cc_final: 0.8044 (t0) REVERT: W 114 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8260 (tt) REVERT: W 294 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7421 (t0) REVERT: X 131 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7748 (ptt-90) REVERT: X 132 ASN cc_start: 0.7890 (t0) cc_final: 0.7673 (t0) outliers start: 147 outliers final: 84 residues processed: 818 average time/residue: 0.5135 time to fit residues: 690.2323 Evaluate side-chains 699 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 607 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 351 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 232 LEU Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 368 VAL Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 294 ASP Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 0.9980 chunk 348 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 457 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 chunk 524 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 551 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 169 ASN C 337 GLN E 169 ASN E 276 GLN E 279 GLN F 26 ASN G 169 ASN G 260 HIS G 337 GLN H 26 ASN L 26 ASN N 26 ASN P 26 ASN Q 382 GLN S 337 GLN S 382 GLN V 78 ASN W 97 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51576 Z= 0.179 Angle : 0.527 7.170 70128 Z= 0.268 Chirality : 0.039 0.142 7800 Planarity : 0.004 0.054 9252 Dihedral : 3.910 24.582 7080 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.41 % Allowed : 12.82 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.11), residues: 6456 helix: 2.68 (0.09), residues: 3228 sheet: 1.03 (0.24), residues: 456 loop : 0.24 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 398 HIS 0.003 0.001 HIS G 260 PHE 0.010 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.010 0.000 ARG I 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 624 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.8399 (tp) cc_final: 0.8059 (tp) REVERT: A 380 MET cc_start: 0.7761 (mmp) cc_final: 0.7497 (mmm) REVERT: B 16 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 54 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: E 149 MET cc_start: 0.6693 (mmm) cc_final: 0.5999 (mmm) REVERT: F 27 LYS cc_start: 0.7332 (tptp) cc_final: 0.6002 (mttp) REVERT: G 229 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8129 (tp) REVERT: G 377 ILE cc_start: 0.7070 (mp) cc_final: 0.6791 (pt) REVERT: H 12 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7472 (tt0) REVERT: H 27 LYS cc_start: 0.7304 (tptp) cc_final: 0.5908 (mttm) REVERT: H 38 ASP cc_start: 0.8291 (m-30) cc_final: 0.8056 (m-30) REVERT: H 49 ASP cc_start: 0.7708 (m-30) cc_final: 0.7302 (m-30) REVERT: I 377 ILE cc_start: 0.7134 (mp) cc_final: 0.6871 (pt) REVERT: L 27 LYS cc_start: 0.7327 (tptp) cc_final: 0.6039 (mttp) REVERT: M 288 MET cc_start: 0.8913 (tpp) cc_final: 0.8335 (tpt) REVERT: O 362 ARG cc_start: 0.6290 (mmm160) cc_final: 0.5854 (mtm180) REVERT: Q 253 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6942 (ttp-110) REVERT: Q 288 MET cc_start: 0.8768 (tpp) cc_final: 0.8327 (tpt) REVERT: S 229 ILE cc_start: 0.8261 (tp) cc_final: 0.7985 (tp) REVERT: T 132 ASN cc_start: 0.8481 (t0) cc_final: 0.8234 (t0) REVERT: U 114 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8005 (tt) REVERT: V 16 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7566 (tt0) REVERT: V 47 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: W 114 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8164 (tt) REVERT: W 294 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7483 (t0) REVERT: X 126 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5337 (mp10) outliers start: 126 outliers final: 87 residues processed: 724 average time/residue: 0.5280 time to fit residues: 625.5070 Evaluate side-chains 676 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 581 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 253 ARG Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 294 ASP Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 1.9990 chunk 553 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 360 optimal weight: 0.0050 chunk 151 optimal weight: 3.9990 chunk 615 optimal weight: 6.9990 chunk 510 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 87 ASN C 169 ASN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN T 126 GLN U 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 51576 Z= 0.382 Angle : 0.683 8.998 70128 Z= 0.350 Chirality : 0.044 0.201 7800 Planarity : 0.006 0.068 9252 Dihedral : 4.640 23.684 7080 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 3.17 % Allowed : 13.09 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.10), residues: 6456 helix: 2.19 (0.09), residues: 3240 sheet: 0.81 (0.23), residues: 456 loop : -0.08 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 398 HIS 0.007 0.001 HIS Q 260 PHE 0.013 0.002 PHE S 32 TYR 0.016 0.002 TYR J 13 ARG 0.022 0.001 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 638 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 132 ASN cc_start: 0.8428 (t0) cc_final: 0.8026 (t0) REVERT: D 67 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8458 (mp) REVERT: D 126 GLN cc_start: 0.6162 (mp10) cc_final: 0.5948 (mm-40) REVERT: E 54 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: F 67 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (mp) REVERT: F 132 ASN cc_start: 0.8464 (t0) cc_final: 0.8140 (t0) REVERT: G 229 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8417 (tp) REVERT: G 377 ILE cc_start: 0.7322 (mp) cc_final: 0.7017 (pt) REVERT: H 12 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7807 (tt0) REVERT: H 38 ASP cc_start: 0.8343 (m-30) cc_final: 0.8068 (m-30) REVERT: I 18 ARG cc_start: 0.7344 (mmt90) cc_final: 0.7125 (mtt-85) REVERT: I 245 ASP cc_start: 0.6840 (m-30) cc_final: 0.6601 (m-30) REVERT: J 69 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7288 (ttt180) REVERT: O 362 ARG cc_start: 0.6530 (mmm160) cc_final: 0.6077 (mtm180) REVERT: Q 377 ILE cc_start: 0.7400 (mp) cc_final: 0.7174 (mt) REVERT: Q 389 ASN cc_start: 0.7428 (m-40) cc_final: 0.7154 (m110) REVERT: R 16 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7492 (tt0) REVERT: S 226 MET cc_start: 0.8276 (ttp) cc_final: 0.7936 (ttm) REVERT: T 19 ARG cc_start: 0.8263 (ttp80) cc_final: 0.8034 (mtm110) REVERT: T 132 ASN cc_start: 0.8839 (t0) cc_final: 0.8563 (t0) REVERT: U 114 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (tt) REVERT: V 16 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7734 (tm-30) REVERT: V 47 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: V 126 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.5328 (mt0) REVERT: X 126 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.5637 (mp10) REVERT: X 131 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7900 (ptt-90) outliers start: 166 outliers final: 106 residues processed: 771 average time/residue: 0.5171 time to fit residues: 651.4980 Evaluate side-chains 697 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 581 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 376 ASP Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 6 ASP Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 LEU Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 126 GLN Chi-restraints excluded: chain W residue 34 GLN Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 208 VAL Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 350 optimal weight: 0.8980 chunk 449 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 518 optimal weight: 0.8980 chunk 343 optimal weight: 4.9990 chunk 613 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 373 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 407 GLN C 184 GLN C 260 HIS ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN H 26 ASN I 260 HIS ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN ** Q 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 337 GLN S 389 ASN S 407 GLN T 126 GLN U 337 GLN W 97 ASN W 164 ASN W 260 HIS ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 389 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51576 Z= 0.184 Angle : 0.537 8.574 70128 Z= 0.276 Chirality : 0.039 0.163 7800 Planarity : 0.005 0.061 9252 Dihedral : 4.165 20.670 7080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.27 % Allowed : 13.93 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.10), residues: 6456 helix: 2.53 (0.09), residues: 3204 sheet: 0.77 (0.22), residues: 492 loop : 0.14 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 398 HIS 0.008 0.001 HIS W 260 PHE 0.010 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.013 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 608 time to evaluate : 4.210 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.8195 (ttp) cc_final: 0.7980 (ttm) REVERT: B 16 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 107 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8237 (mttm) REVERT: B 132 ASN cc_start: 0.8313 (t0) cc_final: 0.8028 (t0) REVERT: C 54 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: D 126 GLN cc_start: 0.5823 (mp10) cc_final: 0.5597 (mm-40) REVERT: E 54 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: F 27 LYS cc_start: 0.7439 (tptp) cc_final: 0.5956 (mttp) REVERT: F 132 ASN cc_start: 0.8330 (t0) cc_final: 0.8054 (t0) REVERT: G 16 GLN cc_start: 0.6941 (pm20) cc_final: 0.6719 (pt0) REVERT: G 229 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8212 (tp) REVERT: G 377 ILE cc_start: 0.7242 (mp) cc_final: 0.6947 (pt) REVERT: H 12 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7738 (tt0) REVERT: H 38 ASP cc_start: 0.8291 (m-30) cc_final: 0.8034 (m-30) REVERT: H 107 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8423 (ttmm) REVERT: H 115 ASP cc_start: 0.5129 (p0) cc_final: 0.4653 (p0) REVERT: I 18 ARG cc_start: 0.7246 (mmt90) cc_final: 0.7041 (mtt-85) REVERT: J 132 ASN cc_start: 0.8425 (t0) cc_final: 0.8069 (t0) REVERT: L 132 ASN cc_start: 0.8425 (t0) cc_final: 0.8221 (t0) REVERT: O 66 ASP cc_start: 0.8441 (m-30) cc_final: 0.8236 (m-30) REVERT: O 362 ARG cc_start: 0.6482 (mmm160) cc_final: 0.6200 (mtp-110) REVERT: Q 288 MET cc_start: 0.8744 (tpp) cc_final: 0.8245 (tpt) REVERT: Q 377 ILE cc_start: 0.7304 (mp) cc_final: 0.7079 (mt) REVERT: Q 389 ASN cc_start: 0.7437 (m-40) cc_final: 0.7165 (m110) REVERT: R 16 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7323 (tt0) REVERT: T 19 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8072 (mtm110) REVERT: T 132 ASN cc_start: 0.8582 (t0) cc_final: 0.8355 (t0) REVERT: V 16 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7010 (tm-30) REVERT: V 20 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6769 (mt-10) REVERT: V 47 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: V 126 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5567 (mp10) REVERT: W 66 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8436 (m-30) REVERT: X 126 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5296 (mp10) outliers start: 119 outliers final: 84 residues processed: 703 average time/residue: 0.5710 time to fit residues: 658.8689 Evaluate side-chains 661 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 570 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain S residue 392 LEU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 126 GLN Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 229 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 366 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 120 optimal weight: 0.0770 chunk 118 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 417 optimal weight: 0.4980 chunk 303 optimal weight: 0.0570 chunk 57 optimal weight: 0.9980 chunk 481 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 407 GLN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN O 260 HIS P 26 ASN S 407 GLN T 53 HIS T 126 GLN U 389 ASN W 276 GLN W 279 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 51576 Z= 0.158 Angle : 0.514 8.292 70128 Z= 0.262 Chirality : 0.038 0.150 7800 Planarity : 0.004 0.065 9252 Dihedral : 3.919 23.304 7080 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.97 % Allowed : 14.39 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.11), residues: 6456 helix: 2.64 (0.09), residues: 3228 sheet: 0.95 (0.24), residues: 456 loop : 0.08 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 211 HIS 0.003 0.001 HIS O 260 PHE 0.009 0.001 PHE G 186 TYR 0.014 0.001 TYR J 13 ARG 0.015 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 590 time to evaluate : 4.297 Fit side-chains revert: symmetry clash REVERT: B 16 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 107 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8185 (mttm) REVERT: B 132 ASN cc_start: 0.8248 (t0) cc_final: 0.8028 (t0) REVERT: C 372 ARG cc_start: 0.6490 (tpp-160) cc_final: 0.6168 (tpp80) REVERT: D 85 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 126 GLN cc_start: 0.5731 (mp10) cc_final: 0.5531 (mm-40) REVERT: D 132 ASN cc_start: 0.8083 (t0) cc_final: 0.7818 (t0) REVERT: E 54 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: F 27 LYS cc_start: 0.7462 (tptp) cc_final: 0.5943 (mttp) REVERT: F 126 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.5108 (mp10) REVERT: F 132 ASN cc_start: 0.8229 (t0) cc_final: 0.7993 (t0) REVERT: G 229 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8120 (tp) REVERT: G 377 ILE cc_start: 0.7237 (mp) cc_final: 0.6913 (pt) REVERT: H 12 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7733 (tt0) REVERT: H 27 LYS cc_start: 0.7684 (tptp) cc_final: 0.6174 (mttm) REVERT: H 38 ASP cc_start: 0.8273 (m-30) cc_final: 0.7978 (m-30) REVERT: H 107 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8425 (ttmm) REVERT: H 115 ASP cc_start: 0.5283 (p0) cc_final: 0.5053 (p0) REVERT: J 132 ASN cc_start: 0.8322 (t0) cc_final: 0.7914 (t0) REVERT: M 377 ILE cc_start: 0.7457 (mp) cc_final: 0.7168 (pt) REVERT: O 362 ARG cc_start: 0.6415 (mmm160) cc_final: 0.6215 (mtp-110) REVERT: O 389 ASN cc_start: 0.7892 (m110) cc_final: 0.7599 (m110) REVERT: Q 377 ILE cc_start: 0.7304 (mp) cc_final: 0.7076 (mt) REVERT: Q 389 ASN cc_start: 0.7514 (m-40) cc_final: 0.7238 (m110) REVERT: R 16 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7236 (tt0) REVERT: S 229 ILE cc_start: 0.8321 (tp) cc_final: 0.7938 (tp) REVERT: T 19 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8089 (mtm110) REVERT: V 47 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: V 126 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5601 (mp10) REVERT: X 126 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5089 (mp10) REVERT: X 131 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7586 (ptt-90) outliers start: 103 outliers final: 90 residues processed: 671 average time/residue: 0.5864 time to fit residues: 648.4006 Evaluate side-chains 663 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 566 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 376 ASP Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain S residue 392 LEU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 126 GLN Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 6.9990 chunk 587 optimal weight: 0.8980 chunk 535 optimal weight: 4.9990 chunk 571 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 448 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 516 optimal weight: 0.0370 chunk 540 optimal weight: 1.9990 chunk 569 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN E 169 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN L 26 ASN N 26 ASN P 26 ASN Q 260 HIS R 126 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.7781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 51576 Z= 0.228 Angle : 0.553 9.154 70128 Z= 0.282 Chirality : 0.040 0.162 7800 Planarity : 0.005 0.069 9252 Dihedral : 4.062 19.027 7080 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 14.55 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.11), residues: 6456 helix: 2.66 (0.09), residues: 3204 sheet: 0.97 (0.24), residues: 456 loop : 0.09 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 398 HIS 0.004 0.001 HIS K 217 PHE 0.009 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.016 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 575 time to evaluate : 4.254 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.8226 (ttp) cc_final: 0.7927 (ttm) REVERT: B 16 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 107 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8211 (mttm) REVERT: B 132 ASN cc_start: 0.8370 (t0) cc_final: 0.8130 (t0) REVERT: C 54 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.6893 (mt0) REVERT: D 85 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7404 (mm-30) REVERT: D 126 GLN cc_start: 0.5860 (mp10) cc_final: 0.5629 (mm-40) REVERT: D 132 ASN cc_start: 0.8246 (t0) cc_final: 0.7995 (t0) REVERT: E 54 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: F 27 LYS cc_start: 0.7426 (tptp) cc_final: 0.5916 (mttp) REVERT: F 47 GLU cc_start: 0.7665 (tt0) cc_final: 0.7447 (tt0) REVERT: F 124 THR cc_start: 0.7494 (m) cc_final: 0.7271 (m) REVERT: F 126 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5186 (mp10) REVERT: F 132 ASN cc_start: 0.8395 (t0) cc_final: 0.8090 (t0) REVERT: G 229 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8248 (tp) REVERT: G 377 ILE cc_start: 0.7325 (mp) cc_final: 0.6983 (pt) REVERT: H 12 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7806 (tt0) REVERT: H 38 ASP cc_start: 0.8314 (m-30) cc_final: 0.8053 (m-30) REVERT: M 377 ILE cc_start: 0.7501 (mp) cc_final: 0.7186 (pt) REVERT: O 362 ARG cc_start: 0.6497 (mmm160) cc_final: 0.6252 (mtp-110) REVERT: O 389 ASN cc_start: 0.7877 (m110) cc_final: 0.7462 (m110) REVERT: Q 377 ILE cc_start: 0.7368 (mp) cc_final: 0.7141 (mt) REVERT: Q 389 ASN cc_start: 0.7525 (m-40) cc_final: 0.7274 (m110) REVERT: R 16 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7374 (tt0) REVERT: R 132 ASN cc_start: 0.8588 (t0) cc_final: 0.8351 (t0) REVERT: S 229 ILE cc_start: 0.8532 (tp) cc_final: 0.8206 (tp) REVERT: T 19 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8057 (mtm110) REVERT: V 47 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: X 57 GLN cc_start: 0.7365 (mt0) cc_final: 0.7159 (mt0) REVERT: X 126 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5278 (mp10) REVERT: X 131 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7531 (ptt-90) outliers start: 119 outliers final: 100 residues processed: 665 average time/residue: 0.5327 time to fit residues: 574.6832 Evaluate side-chains 667 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 560 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 6 ASP Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain S residue 392 LEU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 0.9990 chunk 604 optimal weight: 0.5980 chunk 368 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 419 optimal weight: 0.0970 chunk 633 optimal weight: 2.9990 chunk 583 optimal weight: 5.9990 chunk 504 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 389 optimal weight: 0.6980 chunk 309 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 407 GLN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 HIS L 26 ASN M 110 HIS N 26 ASN P 26 ASN ** S 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51576 Z= 0.168 Angle : 0.521 8.103 70128 Z= 0.266 Chirality : 0.038 0.154 7800 Planarity : 0.005 0.072 9252 Dihedral : 3.908 30.025 7080 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.01 % Allowed : 14.81 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.24 (0.11), residues: 6456 helix: 2.69 (0.09), residues: 3216 sheet: 1.05 (0.24), residues: 456 loop : 0.14 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 211 HIS 0.010 0.001 HIS K 260 PHE 0.009 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.017 0.000 ARG G 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 570 time to evaluate : 4.274 Fit side-chains revert: symmetry clash REVERT: B 16 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 54 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6793 (mt0) REVERT: D 85 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7212 (mm-30) REVERT: D 126 GLN cc_start: 0.5832 (mp10) cc_final: 0.5620 (mm-40) REVERT: D 132 ASN cc_start: 0.8229 (t0) cc_final: 0.7971 (t0) REVERT: E 54 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: F 27 LYS cc_start: 0.7400 (tptp) cc_final: 0.5888 (mttp) REVERT: F 47 GLU cc_start: 0.7654 (tt0) cc_final: 0.7397 (tt0) REVERT: F 126 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5118 (mp10) REVERT: F 132 ASN cc_start: 0.8312 (t0) cc_final: 0.8045 (t0) REVERT: G 229 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8075 (tp) REVERT: G 377 ILE cc_start: 0.7366 (mp) cc_final: 0.7023 (pt) REVERT: H 12 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7762 (tt0) REVERT: H 38 ASP cc_start: 0.8305 (m-30) cc_final: 0.8013 (m-30) REVERT: J 132 ASN cc_start: 0.8414 (t0) cc_final: 0.8209 (t0) REVERT: L 107 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8291 (ttmm) REVERT: M 377 ILE cc_start: 0.7485 (mp) cc_final: 0.7162 (pt) REVERT: O 389 ASN cc_start: 0.7877 (m110) cc_final: 0.7460 (m110) REVERT: P 132 ASN cc_start: 0.8550 (t0) cc_final: 0.8347 (t0) REVERT: Q 377 ILE cc_start: 0.7360 (mp) cc_final: 0.7124 (mt) REVERT: Q 389 ASN cc_start: 0.7542 (m-40) cc_final: 0.7253 (m110) REVERT: R 16 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7271 (tt0) REVERT: S 229 ILE cc_start: 0.8380 (tp) cc_final: 0.7975 (tp) REVERT: T 19 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8071 (mtm110) REVERT: V 47 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: V 85 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7214 (mm-30) REVERT: X 126 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5216 (mp10) REVERT: X 131 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7568 (ptt-90) outliers start: 105 outliers final: 89 residues processed: 655 average time/residue: 0.5358 time to fit residues: 569.6957 Evaluate side-chains 645 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 549 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain S residue 392 LEU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 229 ILE Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 0.8980 chunk 537 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 465 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 505 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 518 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 407 GLN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN ** S 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098701 restraints weight = 97285.866| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.92 r_work: 0.3213 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.7921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 51576 Z= 0.190 Angle : 0.532 8.006 70128 Z= 0.271 Chirality : 0.039 0.163 7800 Planarity : 0.005 0.074 9252 Dihedral : 3.926 26.479 7080 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.08 % Allowed : 14.72 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.11), residues: 6456 helix: 2.69 (0.09), residues: 3216 sheet: 1.07 (0.24), residues: 456 loop : 0.12 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 211 HIS 0.003 0.001 HIS K 217 PHE 0.008 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.017 0.000 ARG G 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12343.94 seconds wall clock time: 213 minutes 9.74 seconds (12789.74 seconds total)