Starting phenix.real_space_refine on Thu Oct 10 06:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/10_2024/8rka_19266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/10_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_19266/10_2024/8rka_19266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/10_2024/8rka_19266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/10_2024/8rka_19266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rka_19266/10_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-5477/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: 9.65, 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: 9.40 Conformation dependent library (CDL) restraints added in 4.9 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: 4.12 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: 14.69 Time building geometry restraints manager: 11.02 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: 8.010 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: 0.040 Extract box with map and model: 1.450 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 70.000 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.880 ------------------------------------------------------------------------------- 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 : 4.210 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: 0.5467 time to fit residues: 1138.8705 Evaluate side-chains 731 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 4.067 ------------------------------------------------------------------------------- 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 : 4.338 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: 0.5195 time to fit residues: 761.4900 Evaluate side-chains 727 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 662 time to evaluate : 4.239 ------------------------------------------------------------------------------- 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: 0.7980 chunk 393 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 578 optimal weight: 1.9990 chunk 625 optimal weight: 0.8980 chunk 515 optimal weight: 0.6980 chunk 573 optimal weight: 0.5980 chunk 197 optimal weight: 0.0970 chunk 464 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 GLN J 12 GLN J 26 ASN K 337 GLN M 110 HIS M 337 GLN R 78 ASN W 97 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 51576 Z= 0.189 Angle : 0.547 8.216 70128 Z= 0.279 Chirality : 0.039 0.186 7800 Planarity : 0.005 0.058 9252 Dihedral : 3.829 29.559 7080 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 1.82 % Allowed : 10.65 % Favored : 87.54 % 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: 2.42 (0.11), residues: 6456 helix: 2.70 (0.09), residues: 3216 sheet: 1.40 (0.24), residues: 456 loop : 0.39 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 398 HIS 0.006 0.001 HIS A 323 PHE 0.011 0.001 PHE I 274 TYR 0.015 0.001 TYR E 230 ARG 0.014 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 865 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 770 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.7176 (mmp) cc_final: 0.6730 (mmm) REVERT: B 16 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 49 ASP cc_start: 0.7418 (m-30) cc_final: 0.6956 (m-30) REVERT: B 74 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8613 (mp) REVERT: D 47 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: E 18 ARG cc_start: 0.6956 (mmt90) cc_final: 0.6720 (tpp-160) REVERT: F 27 LYS cc_start: 0.6696 (tptp) cc_final: 0.5878 (mttt) REVERT: F 49 ASP cc_start: 0.7390 (m-30) cc_final: 0.7074 (m-30) REVERT: G 18 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7190 (mmt180) REVERT: G 149 MET cc_start: 0.6202 (mmm) cc_final: 0.5622 (mmm) REVERT: G 229 ILE cc_start: 0.8511 (tp) cc_final: 0.8151 (tp) REVERT: G 377 ILE cc_start: 0.6952 (mp) cc_final: 0.6683 (pt) REVERT: H 27 LYS cc_start: 0.6660 (tptp) cc_final: 0.5640 (mttt) REVERT: H 38 ASP cc_start: 0.8137 (m-30) cc_final: 0.7834 (m-30) REVERT: H 49 ASP cc_start: 0.7211 (m-30) cc_final: 0.6851 (m-30) REVERT: I 377 ILE cc_start: 0.7116 (mp) cc_final: 0.6810 (pt) REVERT: J 23 ASP cc_start: 0.6547 (t70) cc_final: 0.5764 (t70) REVERT: J 27 LYS cc_start: 0.7106 (tptp) cc_final: 0.5866 (mttm) REVERT: J 45 ASP cc_start: 0.8251 (m-30) cc_final: 0.7804 (m-30) REVERT: K 288 MET cc_start: 0.8533 (tpp) cc_final: 0.7564 (tpt) REVERT: L 27 LYS cc_start: 0.7193 (tptp) cc_final: 0.5911 (mttm) REVERT: M 144 GLN cc_start: 0.6622 (mp10) cc_final: 0.6400 (mt0) REVERT: N 46 SER cc_start: 0.8830 (m) cc_final: 0.8560 (m) REVERT: O 144 GLN cc_start: 0.6919 (mp10) cc_final: 0.6630 (mt0) REVERT: Q 288 MET cc_start: 0.8830 (tpp) cc_final: 0.8296 (tpt) REVERT: T 132 ASN cc_start: 0.8477 (t0) cc_final: 0.8118 (t0) REVERT: U 114 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7839 (tt) REVERT: U 380 MET cc_start: 0.7575 (mmm) cc_final: 0.6831 (mmm) REVERT: W 114 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8017 (tt) outliers start: 95 outliers final: 53 residues processed: 830 average time/residue: 0.5447 time to fit residues: 747.2100 Evaluate side-chains 723 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 666 time to evaluate : 4.224 ------------------------------------------------------------------------------- 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 197 SER 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 50 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 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 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 109 SER Chi-restraints excluded: chain O residue 230 TYR 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 197 SER 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 T residue 60 LEU 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 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: 0.0470 chunk 435 optimal weight: 0.0470 chunk 300 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 388 optimal weight: 0.1980 chunk 580 optimal weight: 3.9990 chunk 614 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 550 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 HIS J 26 ASN L 26 ASN M 97 ASN Q 382 GLN R 78 ASN W 97 ASN W 164 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 51576 Z= 0.149 Angle : 0.509 6.315 70128 Z= 0.259 Chirality : 0.038 0.158 7800 Planarity : 0.004 0.050 9252 Dihedral : 3.683 25.640 7080 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.12 % Allowed : 11.85 % Favored : 86.03 % 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: 2.39 (0.11), residues: 6456 helix: 2.71 (0.09), residues: 3240 sheet: 1.30 (0.24), residues: 456 loop : 0.30 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 348 HIS 0.008 0.001 HIS Q 260 PHE 0.019 0.001 PHE G 186 TYR 0.020 0.001 TYR A 230 ARG 0.012 0.000 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 821 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 710 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.7282 (mmp) cc_final: 0.6971 (mmm) REVERT: D 23 ASP cc_start: 0.6441 (t0) cc_final: 0.6209 (t0) REVERT: D 47 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: E 149 MET cc_start: 0.6374 (mmm) cc_final: 0.6067 (mmm) REVERT: E 273 ASP cc_start: 0.7253 (p0) cc_final: 0.6942 (p0) REVERT: F 16 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7981 (tm-30) REVERT: F 27 LYS cc_start: 0.6886 (tptp) cc_final: 0.5924 (mttt) REVERT: G 149 MET cc_start: 0.6421 (mmm) cc_final: 0.6181 (mmm) REVERT: G 229 ILE cc_start: 0.8476 (tp) cc_final: 0.8119 (tp) REVERT: G 273 ASP cc_start: 0.6462 (m-30) cc_final: 0.6240 (m-30) REVERT: G 377 ILE cc_start: 0.6841 (mp) cc_final: 0.6568 (pt) REVERT: H 12 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7008 (tt0) REVERT: H 16 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7155 (tm-30) REVERT: H 27 LYS cc_start: 0.6612 (tptp) cc_final: 0.5654 (mttt) REVERT: H 38 ASP cc_start: 0.8117 (m-30) cc_final: 0.7873 (m-30) REVERT: H 49 ASP cc_start: 0.7207 (m-30) cc_final: 0.6850 (m-30) REVERT: I 377 ILE cc_start: 0.7112 (mp) cc_final: 0.6814 (pt) REVERT: J 27 LYS cc_start: 0.6974 (tptp) cc_final: 0.5714 (mttm) REVERT: J 45 ASP cc_start: 0.8287 (m-30) cc_final: 0.7859 (m-30) REVERT: K 288 MET cc_start: 0.8658 (tpp) cc_final: 0.7629 (tpt) REVERT: L 27 LYS cc_start: 0.7296 (tptp) cc_final: 0.6021 (mttp) REVERT: M 288 MET cc_start: 0.8773 (tpp) cc_final: 0.8424 (tpt) REVERT: N 46 SER cc_start: 0.8873 (m) cc_final: 0.8633 (m) REVERT: Q 288 MET cc_start: 0.8820 (tpp) cc_final: 0.8325 (tpt) REVERT: R 107 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7508 (mtmm) REVERT: T 132 ASN cc_start: 0.8413 (t0) cc_final: 0.8115 (t0) REVERT: U 114 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (tt) REVERT: W 114 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8133 (tt) REVERT: W 229 ILE cc_start: 0.7748 (tp) cc_final: 0.7519 (tp) REVERT: W 294 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7213 (t0) outliers start: 111 outliers final: 70 residues processed: 793 average time/residue: 0.4982 time to fit residues: 650.6484 Evaluate side-chains 720 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 645 time to evaluate : 4.246 ------------------------------------------------------------------------------- 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 21 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 122 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 15 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain J residue 34 THR 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 351 LEU 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 230 TYR 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 67 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 65 THR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 107 LYS Chi-restraints excluded: chain S residue 6 ASP 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 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 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 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 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: 6.9990 chunk 8 optimal weight: 0.8980 chunk 457 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 524 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 551 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 337 GLN B 87 ASN C 276 GLN C 337 GLN E 276 GLN E 279 GLN F 126 GLN H 126 GLN J 26 ASN J 53 HIS K 191 HIS L 26 ASN L 126 GLN N 126 GLN O 337 GLN Q 389 ASN S 337 GLN W 97 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 51576 Z= 0.393 Angle : 0.712 9.451 70128 Z= 0.365 Chirality : 0.046 0.173 7800 Planarity : 0.006 0.067 9252 Dihedral : 4.737 25.852 7080 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 3.13 % Allowed : 12.39 % Favored : 84.48 % 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: 1.74 (0.10), residues: 6456 helix: 2.15 (0.09), residues: 3228 sheet: 0.70 (0.21), residues: 576 loop : 0.06 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 398 HIS 0.009 0.001 HIS K 217 PHE 0.015 0.002 PHE E 32 TYR 0.023 0.002 TYR A 230 ARG 0.008 0.001 ARG V 131 *********************** 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 845 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 681 time to evaluate : 4.344 Fit side-chains revert: symmetry clash REVERT: B 132 ASN cc_start: 0.8176 (t0) cc_final: 0.7928 (t0) REVERT: D 67 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (mp) REVERT: E 54 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: E 149 MET cc_start: 0.6813 (mmm) cc_final: 0.6598 (mmm) REVERT: F 27 LYS cc_start: 0.7340 (tptp) cc_final: 0.5906 (mttp) REVERT: F 67 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (mp) REVERT: G 229 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8437 (tp) REVERT: G 377 ILE cc_start: 0.7213 (mp) cc_final: 0.6952 (pt) REVERT: H 12 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7723 (tt0) REVERT: H 38 ASP cc_start: 0.8417 (m-30) cc_final: 0.8191 (m-30) REVERT: H 115 ASP cc_start: 0.4611 (p0) cc_final: 0.4267 (p0) REVERT: I 18 ARG cc_start: 0.7315 (mmt90) cc_final: 0.7087 (mtt-85) REVERT: J 69 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7290 (ttt180) REVERT: K 288 MET cc_start: 0.9018 (tpp) cc_final: 0.8388 (tpt) REVERT: M 144 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: Q 377 ILE cc_start: 0.7225 (mp) cc_final: 0.7016 (mt) REVERT: R 98 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8174 (pttp) REVERT: S 226 MET cc_start: 0.8302 (ttp) cc_final: 0.7951 (ttm) REVERT: T 132 ASN cc_start: 0.8771 (t0) cc_final: 0.8491 (t0) REVERT: U 114 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8271 (tt) REVERT: V 16 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7409 (tt0) REVERT: V 43 ASP cc_start: 0.8351 (m-30) cc_final: 0.7852 (m-30) REVERT: V 50 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8832 (mp) REVERT: W 114 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8251 (tt) REVERT: X 126 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: X 131 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7811 (ptt-90) REVERT: X 132 ASN cc_start: 0.8299 (t0) cc_final: 0.7985 (t0) outliers start: 164 outliers final: 99 residues processed: 807 average time/residue: 0.5132 time to fit residues: 674.7292 Evaluate side-chains 705 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 595 time to evaluate : 4.269 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 387 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 C residue 41 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 ILE 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 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 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR 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 341 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain K residue 151 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 341 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 34 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 86 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 50 LEU 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 229 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 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 401 ASP Chi-restraints excluded: chain R residue 2 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 R residue 50 LEU 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 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 U residue 305 LEU Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 50 LEU 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 114 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 273 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 50 LEU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 0.8980 chunk 553 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 151 optimal weight: 0.0970 chunk 615 optimal weight: 4.9990 chunk 510 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 323 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 407 GLN E 169 ASN E 260 HIS F 26 ASN G 169 ASN G 337 GLN L 26 ASN N 26 ASN O 382 GLN P 26 ASN Q 260 HIS Q 337 GLN W 97 ASN W 164 ASN W 276 GLN W 337 GLN W 407 GLN X 26 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 51576 Z= 0.164 Angle : 0.531 6.667 70128 Z= 0.272 Chirality : 0.038 0.143 7800 Planarity : 0.004 0.056 9252 Dihedral : 4.107 22.373 7080 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.97 % Allowed : 14.51 % Favored : 83.52 % 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: 2.12 (0.10), residues: 6456 helix: 2.53 (0.09), residues: 3216 sheet: 0.88 (0.22), residues: 492 loop : 0.18 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 398 HIS 0.010 0.001 HIS E 260 PHE 0.009 0.001 PHE A 285 TYR 0.014 0.001 TYR J 13 ARG 0.013 0.000 ARG I 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 736 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 633 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7526 (t0) REVERT: B 107 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8298 (mttm) REVERT: B 126 GLN cc_start: 0.6151 (mp10) cc_final: 0.5877 (mm-40) REVERT: B 132 ASN cc_start: 0.8051 (t0) cc_final: 0.7737 (t0) REVERT: C 54 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.6746 (mt0) REVERT: E 149 MET cc_start: 0.6822 (mmm) cc_final: 0.6143 (mmm) REVERT: F 27 LYS cc_start: 0.7357 (tptp) cc_final: 0.5907 (mttp) REVERT: G 229 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8040 (tp) REVERT: G 377 ILE cc_start: 0.7273 (mp) cc_final: 0.7016 (pt) REVERT: H 12 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7671 (tt0) REVERT: H 20 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6760 (mt-10) REVERT: H 27 LYS cc_start: 0.7435 (tptp) cc_final: 0.6038 (mttm) REVERT: H 38 ASP cc_start: 0.8368 (m-30) cc_final: 0.8116 (m-30) REVERT: H 49 ASP cc_start: 0.7832 (m-30) cc_final: 0.7592 (m-30) REVERT: I 18 ARG cc_start: 0.7300 (mmt90) cc_final: 0.7063 (mtt-85) REVERT: I 226 MET cc_start: 0.8183 (ttp) cc_final: 0.7928 (ttm) REVERT: O 66 ASP cc_start: 0.8363 (m-30) cc_final: 0.8142 (m-30) REVERT: O 362 ARG cc_start: 0.6412 (mmm160) cc_final: 0.6018 (mtm180) REVERT: Q 288 MET cc_start: 0.8907 (tpp) cc_final: 0.8245 (tpt) REVERT: R 16 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7379 (tt0) REVERT: S 407 GLN cc_start: 0.5764 (mm110) cc_final: 0.5506 (mm-40) REVERT: T 19 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8059 (ttp80) REVERT: T 132 ASN cc_start: 0.8541 (t0) cc_final: 0.8334 (t0) REVERT: V 16 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7400 (tt0) REVERT: V 126 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.5633 (mp10) REVERT: V 132 ASN cc_start: 0.8442 (t0) cc_final: 0.8227 (t0) REVERT: W 66 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: X 126 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5280 (mp10) REVERT: X 132 ASN cc_start: 0.8139 (t0) cc_final: 0.7891 (t0) outliers start: 103 outliers final: 61 residues processed: 718 average time/residue: 0.5165 time to fit residues: 603.0098 Evaluate side-chains 653 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 586 time to evaluate : 4.283 ------------------------------------------------------------------------------- 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 197 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 305 LEU 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 C residue 54 GLN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR 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 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 35 VAL Chi-restraints excluded: chain J residue 67 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 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 M residue 305 LEU Chi-restraints excluded: chain M residue 376 ASP 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 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 P residue 82 VAL Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 376 ASP 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 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 197 SER Chi-restraints excluded: chain U residue 229 ILE Chi-restraints excluded: chain V residue 2 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 350 optimal weight: 2.9990 chunk 449 optimal weight: 0.8980 chunk 348 optimal weight: 9.9990 chunk 518 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 613 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 373 optimal weight: 0.9990 chunk 283 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN C 169 ASN F 26 ASN L 26 ASN N 26 ASN O 260 HIS P 26 ASN Q 389 ASN T 126 GLN ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 97 ASN W 276 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7433 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= 0.232 Angle : 0.563 7.848 70128 Z= 0.288 Chirality : 0.040 0.174 7800 Planarity : 0.005 0.063 9252 Dihedral : 4.132 20.820 7080 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.37 % Allowed : 14.43 % 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: 2.08 (0.11), residues: 6456 helix: 2.56 (0.09), residues: 3228 sheet: 0.93 (0.24), residues: 456 loop : 0.08 (0.12), residues: 2772 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 0.007 0.001 PHE Q 285 TYR 0.014 0.001 TYR J 13 ARG 0.016 0.001 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 733 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 609 time to evaluate : 4.563 Fit side-chains REVERT: B 107 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8313 (mttm) REVERT: B 126 GLN cc_start: 0.6282 (mp10) cc_final: 0.6036 (mm-40) REVERT: B 132 ASN cc_start: 0.8254 (t0) cc_final: 0.8016 (t0) REVERT: E 54 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: E 149 MET cc_start: 0.6853 (mmm) cc_final: 0.6154 (mmm) REVERT: F 27 LYS cc_start: 0.7451 (tptp) cc_final: 0.5944 (mttp) REVERT: G 229 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8195 (tp) REVERT: G 377 ILE cc_start: 0.7201 (mp) cc_final: 0.6879 (pt) REVERT: H 12 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7739 (tt0) REVERT: H 20 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6777 (mt-10) REVERT: H 38 ASP cc_start: 0.8407 (m-30) cc_final: 0.8167 (m-30) REVERT: I 18 ARG cc_start: 0.7251 (mmt90) cc_final: 0.7047 (mtt-85) REVERT: O 362 ARG cc_start: 0.6505 (mmm160) cc_final: 0.6116 (mtp-110) REVERT: Q 288 MET cc_start: 0.8892 (tpp) cc_final: 0.8234 (tpt) REVERT: Q 377 ILE cc_start: 0.7295 (mp) cc_final: 0.7062 (mt) REVERT: R 16 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7373 (tt0) REVERT: R 132 ASN cc_start: 0.8630 (t0) cc_final: 0.8342 (t0) REVERT: S 407 GLN cc_start: 0.5721 (mm110) cc_final: 0.5471 (mm-40) REVERT: T 132 ASN cc_start: 0.8589 (t0) cc_final: 0.8346 (t0) REVERT: V 126 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.5691 (mp10) REVERT: W 66 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: X 126 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5293 (mp10) REVERT: X 132 ASN cc_start: 0.8317 (t0) cc_final: 0.8078 (t0) outliers start: 124 outliers final: 90 residues processed: 701 average time/residue: 0.5543 time to fit residues: 637.7687 Evaluate side-chains 674 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 579 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 67 MET 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 87 ASN Chi-restraints excluded: chain C residue 41 THR 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 D residue 22 SER 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 67 LEU Chi-restraints excluded: chain F residue 107 LYS 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 I residue 229 ILE 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 67 LEU 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 305 LEU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 66 ASP Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 305 LEU Chi-restraints excluded: chain M residue 376 ASP Chi-restraints excluded: chain N residue 2 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 234 ILE 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 P residue 82 VAL Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 376 ASP 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 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 197 SER Chi-restraints excluded: chain V residue 2 SER 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 305 LEU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain W residue 390 VAL 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 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: 1.9990 chunk 366 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 389 optimal weight: 0.6980 chunk 417 optimal weight: 0.0670 chunk 303 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 481 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** I 260 HIS K 260 HIS L 26 ASN N 26 ASN P 26 ASN S 389 ASN T 126 GLN U 276 GLN W 164 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 51576 Z= 0.168 Angle : 0.519 10.097 70128 Z= 0.265 Chirality : 0.038 0.146 7800 Planarity : 0.004 0.065 9252 Dihedral : 3.944 19.758 7080 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.03 % Allowed : 15.08 % Favored : 82.89 % 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: 2.67 (0.09), residues: 3216 sheet: 0.95 (0.24), residues: 456 loop : 0.20 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 211 HIS 0.009 0.001 HIS K 260 PHE 0.007 0.001 PHE Q 285 TYR 0.013 0.001 TYR J 13 ARG 0.013 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 695 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 589 time to evaluate : 4.445 Fit side-chains REVERT: B 107 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8247 (mttm) REVERT: B 126 GLN cc_start: 0.6095 (mp10) cc_final: 0.5804 (mm-40) REVERT: C 54 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6741 (mt0) REVERT: E 54 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: E 149 MET cc_start: 0.6837 (mmm) cc_final: 0.6112 (mmm) REVERT: F 27 LYS cc_start: 0.7412 (tptp) cc_final: 0.5904 (mttp) REVERT: F 47 GLU cc_start: 0.7735 (tt0) cc_final: 0.7531 (tt0) REVERT: G 229 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (tp) REVERT: G 377 ILE cc_start: 0.7219 (mp) cc_final: 0.6904 (pt) REVERT: H 12 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7745 (tt0) REVERT: H 38 ASP cc_start: 0.8436 (m-30) cc_final: 0.8203 (m-30) REVERT: O 253 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6952 (ttp-110) REVERT: O 362 ARG cc_start: 0.6483 (mmm160) cc_final: 0.6184 (mtp-110) REVERT: P 132 ASN cc_start: 0.8614 (t0) cc_final: 0.8348 (t0) REVERT: Q 253 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6824 (ttp-110) REVERT: Q 288 MET cc_start: 0.8830 (tpp) cc_final: 0.8155 (tpt) REVERT: Q 377 ILE cc_start: 0.7292 (mp) cc_final: 0.7059 (mt) REVERT: R 16 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7299 (tt0) REVERT: S 229 ILE cc_start: 0.8340 (tp) cc_final: 0.7979 (tp) REVERT: S 407 GLN cc_start: 0.5868 (mm110) cc_final: 0.5624 (mm-40) REVERT: V 126 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.5628 (mp10) REVERT: X 126 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5117 (mp10) REVERT: X 131 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7455 (ptt-90) outliers start: 106 outliers final: 84 residues processed: 670 average time/residue: 0.5311 time to fit residues: 576.5567 Evaluate side-chains 656 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 566 time to evaluate : 4.394 ------------------------------------------------------------------------------- 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 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 87 ASN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 2 SER 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 2 SER 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 107 LYS 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 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 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 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 66 ASP 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 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 65 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain Q residue 6 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 197 SER Chi-restraints excluded: chain U residue 276 GLN Chi-restraints excluded: chain V residue 2 SER 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 67 MET 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 W residue 390 VAL 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 98 LYS 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: 2.9990 chunk 587 optimal weight: 0.8980 chunk 535 optimal weight: 0.9980 chunk 571 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 448 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 516 optimal weight: 0.0980 chunk 540 optimal weight: 0.9990 chunk 569 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 L 26 ASN N 26 ASN P 26 ASN Q 389 ASN T 126 GLN U 276 GLN V 78 ASN W 260 HIS W 407 GLN X 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 51576 Z= 0.163 Angle : 0.519 8.951 70128 Z= 0.265 Chirality : 0.038 0.160 7800 Planarity : 0.004 0.071 9252 Dihedral : 3.856 18.886 7080 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.99 % Allowed : 15.16 % Favored : 82.86 % 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: 2.24 (0.11), residues: 6456 helix: 2.70 (0.09), residues: 3228 sheet: 1.00 (0.24), residues: 456 loop : 0.14 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 211 HIS 0.007 0.001 HIS W 260 PHE 0.008 0.001 PHE U 274 TYR 0.012 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 693 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 589 time to evaluate : 4.360 Fit side-chains REVERT: B 107 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8234 (mttm) REVERT: B 126 GLN cc_start: 0.6064 (mp10) cc_final: 0.5791 (mm-40) REVERT: C 54 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: C 229 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7909 (tp) REVERT: E 54 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: E 149 MET cc_start: 0.6801 (mmm) cc_final: 0.6122 (mmm) REVERT: F 27 LYS cc_start: 0.7411 (tptp) cc_final: 0.5876 (mttp) REVERT: F 47 GLU cc_start: 0.7763 (tt0) cc_final: 0.7559 (tt0) REVERT: G 229 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (tp) REVERT: G 377 ILE cc_start: 0.7188 (mp) cc_final: 0.6868 (pt) REVERT: H 12 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7746 (tt0) REVERT: H 38 ASP cc_start: 0.8445 (m-30) cc_final: 0.8210 (m-30) REVERT: L 107 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8331 (ttmm) REVERT: M 377 ILE cc_start: 0.7457 (mp) cc_final: 0.7166 (pt) REVERT: O 362 ARG cc_start: 0.6465 (mmm160) cc_final: 0.6217 (mtp-110) REVERT: P 132 ASN cc_start: 0.8546 (t0) cc_final: 0.8247 (t0) REVERT: Q 253 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6832 (ttp-110) REVERT: Q 377 ILE cc_start: 0.7343 (mp) cc_final: 0.7107 (mt) REVERT: R 16 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7342 (tt0) REVERT: S 229 ILE cc_start: 0.8301 (tp) cc_final: 0.7921 (tp) REVERT: V 126 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.5671 (mp10) REVERT: X 126 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5144 (mp10) REVERT: X 131 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7517 (ptt-90) outliers start: 104 outliers final: 89 residues processed: 667 average time/residue: 0.5197 time to fit residues: 565.3029 Evaluate side-chains 668 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 572 time to evaluate : 4.299 ------------------------------------------------------------------------------- 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 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 C residue 41 THR Chi-restraints excluded: chain C residue 54 GLN 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 D residue 2 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 VAL 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 2 SER 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 107 LYS 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 I residue 229 ILE 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 11 GLU 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 305 LEU 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 66 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 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 65 THR Chi-restraints excluded: chain P residue 82 VAL 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 11 GLU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain S residue 67 MET 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 107 LYS Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER 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 67 MET 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 47 GLU Chi-restraints excluded: chain X residue 60 LEU 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: 1.9990 chunk 604 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 419 optimal weight: 0.6980 chunk 633 optimal weight: 2.9990 chunk 583 optimal weight: 5.9990 chunk 504 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 389 optimal weight: 0.0770 chunk 309 optimal weight: 3.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 169 ASN C 169 ASN E 169 ASN L 26 ASN N 26 ASN P 26 ASN R 126 GLN U 276 GLN V 78 ASN W 407 GLN X 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 51576 Z= 0.230 Angle : 0.562 9.012 70128 Z= 0.287 Chirality : 0.040 0.167 7800 Planarity : 0.005 0.071 9252 Dihedral : 4.083 27.921 7080 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.82 % Rotamer: Outliers : 2.10 % Allowed : 15.16 % Favored : 82.74 % 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: 2.18 (0.11), residues: 6456 helix: 2.65 (0.09), residues: 3216 sheet: 1.00 (0.24), residues: 456 loop : 0.11 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 398 HIS 0.005 0.001 HIS W 260 PHE 0.009 0.001 PHE O 285 TYR 0.013 0.001 TYR J 13 ARG 0.016 0.001 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 700 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 590 time to evaluate : 4.268 Fit side-chains REVERT: B 107 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8305 (mttm) REVERT: B 126 GLN cc_start: 0.6176 (mp10) cc_final: 0.5946 (mm-40) REVERT: C 54 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: E 54 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: E 149 MET cc_start: 0.6759 (mmm) cc_final: 0.6085 (mmm) REVERT: F 27 LYS cc_start: 0.7369 (tptp) cc_final: 0.5810 (mttp) REVERT: G 229 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8214 (tp) REVERT: G 377 ILE cc_start: 0.7361 (mp) cc_final: 0.7011 (pt) REVERT: H 12 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7813 (tt0) REVERT: H 38 ASP cc_start: 0.8441 (m-30) cc_final: 0.8214 (m-30) REVERT: K 362 ARG cc_start: 0.6392 (mmm160) cc_final: 0.6119 (ttm-80) REVERT: M 229 ILE cc_start: 0.8474 (tp) cc_final: 0.8244 (tp) REVERT: M 377 ILE cc_start: 0.7501 (mp) cc_final: 0.7178 (pt) REVERT: O 362 ARG cc_start: 0.6546 (mmm160) cc_final: 0.6275 (mtp-110) REVERT: P 132 ASN cc_start: 0.8602 (t0) cc_final: 0.8333 (t0) REVERT: Q 253 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6857 (ttp-110) REVERT: Q 377 ILE cc_start: 0.7368 (mp) cc_final: 0.7139 (mt) REVERT: R 16 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7374 (tt0) REVERT: R 107 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8360 (ttmm) REVERT: S 229 ILE cc_start: 0.8561 (tp) cc_final: 0.8239 (tp) REVERT: S 407 GLN cc_start: 0.5659 (mm110) cc_final: 0.5414 (mm-40) REVERT: V 85 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7190 (mm-30) REVERT: V 126 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.5800 (mp10) REVERT: W 66 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8435 (m-30) REVERT: X 126 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5334 (mp10) REVERT: X 131 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7689 (ptt-90) REVERT: X 132 ASN cc_start: 0.7981 (t0) cc_final: 0.7771 (t0) outliers start: 110 outliers final: 93 residues processed: 671 average time/residue: 0.5224 time to fit residues: 571.0198 Evaluate side-chains 673 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 573 time to evaluate : 4.318 ------------------------------------------------------------------------------- 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 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 C residue 41 THR Chi-restraints excluded: chain C residue 54 GLN 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 D residue 2 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 VAL 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 2 SER 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 107 LYS 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 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 65 THR Chi-restraints excluded: chain J residue 67 LEU 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 305 LEU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 66 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 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 P residue 2 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 VAL 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 67 MET 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 197 SER Chi-restraints excluded: chain U residue 279 GLN Chi-restraints excluded: chain V residue 2 SER 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 208 VAL 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 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: 4.9990 chunk 537 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 465 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 505 optimal weight: 0.9990 chunk 211 optimal weight: 0.0970 chunk 518 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN L 26 ASN M 110 HIS N 26 ASN P 26 ASN U 337 GLN W 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099407 restraints weight = 97208.851| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.92 r_work: 0.3225 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51576 Z= 0.177 Angle : 0.530 8.751 70128 Z= 0.271 Chirality : 0.039 0.160 7800 Planarity : 0.005 0.073 9252 Dihedral : 3.926 20.474 7080 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.05 % Allowed : 15.33 % Favored : 82.63 % 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: 2.24 (0.11), residues: 6456 helix: 2.68 (0.09), residues: 3216 sheet: 1.02 (0.24), residues: 456 loop : 0.17 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 398 HIS 0.003 0.001 HIS I 323 PHE 0.007 0.001 PHE O 285 TYR 0.013 0.001 TYR J 13 ARG 0.019 0.000 ARG A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12094.00 seconds wall clock time: 212 minutes 20.70 seconds (12740.70 seconds total)