Starting phenix.real_space_refine on Wed Jan 15 00:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_19266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_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/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_19266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_19266.map" model { file = "/net/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_19266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rka_19266/01_2025/8rka_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-5571/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: 9.77, 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: 9.71 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: 3.79 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: 16.06 Time building geometry restraints manager: 11.45 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: 0.33 Found NCS groups: 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' } 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' } 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: 6.130 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: 0.060 Extract box with map and model: 1.700 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 72.730 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.240 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.620 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 1316 time to evaluate : 4.404 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: 0.5553 time to fit residues: 1156.6950 Evaluate side-chains 731 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 731 time to evaluate : 4.164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108860 restraints weight = 96273.564| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.99 r_work: 0.3375 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 to be fit. rotamer outliers: 108 poor density : 836 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7851 (t0) REVERT: B 74 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8223 (mp) REVERT: D 27 LYS cc_start: 0.6469 (tptp) cc_final: 0.5688 (mttm) REVERT: E 18 ARG cc_start: 0.7060 (mmt90) cc_final: 0.6753 (tpp-160) REVERT: E 56 ASN cc_start: 0.6807 (t0) cc_final: 0.6575 (t0) REVERT: E 304 THR cc_start: 0.5284 (OUTLIER) cc_final: 0.4854 (m) REVERT: F 27 LYS cc_start: 0.6110 (tptp) cc_final: 0.5357 (mttt) REVERT: F 49 ASP cc_start: 0.7320 (m-30) cc_final: 0.6991 (m-30) REVERT: G 149 MET cc_start: 0.6185 (mmm) cc_final: 0.5614 (mmm) REVERT: G 377 ILE cc_start: 0.7039 (mp) cc_final: 0.6792 (tt) REVERT: H 27 LYS cc_start: 0.6310 (tptp) cc_final: 0.5237 (mttt) REVERT: H 49 ASP cc_start: 0.7183 (m-30) cc_final: 0.6918 (m-30) REVERT: I 67 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: I 377 ILE cc_start: 0.7301 (mp) cc_final: 0.7055 (pt) REVERT: J 27 LYS cc_start: 0.6918 (tptp) cc_final: 0.5479 (mttm) REVERT: J 45 ASP cc_start: 0.8300 (m-30) cc_final: 0.8077 (m-30) REVERT: J 51 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7343 (t-90) REVERT: J 115 ASP cc_start: 0.4855 (p0) cc_final: 0.4423 (p0) REVERT: K 65 MET cc_start: 0.8521 (mtt) cc_final: 0.8075 (mtt) REVERT: K 273 ASP cc_start: 0.7523 (p0) cc_final: 0.6965 (p0) REVERT: L 27 LYS cc_start: 0.7278 (tptp) cc_final: 0.5714 (mttm) REVERT: L 38 ASP cc_start: 0.8688 (m-30) cc_final: 0.8469 (m-30) REVERT: M 96 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6419 (ttp-110) REVERT: M 144 GLN cc_start: 0.6774 (mp10) cc_final: 0.6351 (mt0) REVERT: N 27 LYS cc_start: 0.7174 (tptp) cc_final: 0.5278 (mttm) REVERT: O 96 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6436 (ttp-110) REVERT: O 144 GLN cc_start: 0.6957 (mp10) cc_final: 0.6508 (mt0) REVERT: O 392 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8179 (mp) REVERT: S 288 MET cc_start: 0.8807 (tpp) cc_final: 0.8606 (tpt) REVERT: T 132 ASN cc_start: 0.8204 (t0) cc_final: 0.7923 (t0) REVERT: U 273 ASP cc_start: 0.6938 (p0) cc_final: 0.6713 (p0) REVERT: U 380 MET cc_start: 0.7549 (mmm) cc_final: 0.6902 (mmm) REVERT: V 20 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7075 (mt-10) REVERT: V 132 ASN cc_start: 0.7533 (t0) cc_final: 0.7292 (t0) REVERT: W 294 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7818 (t0) REVERT: X 126 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.5939 (mp10) outliers start: 108 outliers final: 60 residues processed: 903 average time/residue: 0.5249 time to fit residues: 770.0866 Evaluate side-chains 732 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 662 time to evaluate : 4.176 ------------------------------------------------------------------------------- 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 294 ASP 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 E residue 304 THR 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 67 MET 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 96 ARG 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 O residue 392 LEU 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 427 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 463 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 590 optimal weight: 0.7980 chunk 566 optimal weight: 0.7980 chunk 445 optimal weight: 0.7980 chunk 268 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN C 164 ASN C 184 GLN C 276 GLN E 184 GLN I 276 GLN I 337 GLN J 12 GLN J 26 ASN K 337 GLN M 110 HIS M 337 GLN N 126 GLN R 78 ASN W 97 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106234 restraints weight = 96714.454| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.00 r_work: 0.3334 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 51576 Z= 0.204 Angle : 0.569 8.148 70128 Z= 0.290 Chirality : 0.040 0.203 7800 Planarity : 0.005 0.086 9252 Dihedral : 3.915 30.641 7080 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 1.99 % Allowed : 10.74 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.11), residues: 6456 helix: 2.66 (0.09), residues: 3216 sheet: 1.36 (0.24), residues: 456 loop : 0.34 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 398 HIS 0.006 0.001 HIS A 323 PHE 0.017 0.001 PHE K 206 TYR 0.015 0.001 TYR X 13 ARG 0.013 0.001 ARG G 253 *********************** 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 859 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 755 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: A 380 MET cc_start: 0.7415 (mmp) cc_final: 0.7206 (mmm) REVERT: B 16 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8575 (tm-30) REVERT: B 49 ASP cc_start: 0.7945 (m-30) cc_final: 0.7563 (m-30) REVERT: C 304 THR cc_start: 0.5896 (OUTLIER) cc_final: 0.5513 (m) REVERT: D 47 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: E 18 ARG cc_start: 0.7236 (mmt90) cc_final: 0.6875 (tpp-160) REVERT: E 149 MET cc_start: 0.6850 (mmm) cc_final: 0.6608 (mmm) REVERT: E 253 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.7116 (mtm110) REVERT: E 304 THR cc_start: 0.5409 (OUTLIER) cc_final: 0.5116 (m) REVERT: F 27 LYS cc_start: 0.6767 (tptp) cc_final: 0.5647 (mttm) REVERT: F 49 ASP cc_start: 0.7802 (m-30) cc_final: 0.7548 (m-30) REVERT: G 229 ILE cc_start: 0.8639 (tp) cc_final: 0.8260 (tp) REVERT: G 377 ILE cc_start: 0.7253 (mp) cc_final: 0.6998 (pt) REVERT: H 38 ASP cc_start: 0.8596 (m-30) cc_final: 0.8378 (m-30) REVERT: H 49 ASP cc_start: 0.7648 (m-30) cc_final: 0.7338 (m-30) REVERT: I 67 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: I 377 ILE cc_start: 0.7452 (mp) cc_final: 0.7158 (pt) REVERT: J 27 LYS cc_start: 0.7152 (tptp) cc_final: 0.5619 (mttm) REVERT: J 45 ASP cc_start: 0.8541 (m-30) cc_final: 0.8104 (m-30) REVERT: K 245 ASP cc_start: 0.6745 (m-30) cc_final: 0.6376 (m-30) REVERT: K 288 MET cc_start: 0.8679 (tpp) cc_final: 0.7710 (tpt) REVERT: L 27 LYS cc_start: 0.7358 (tptp) cc_final: 0.5787 (mttp) REVERT: M 144 GLN cc_start: 0.6773 (mp10) cc_final: 0.6520 (mt0) REVERT: Q 288 MET cc_start: 0.9027 (tpp) cc_final: 0.8671 (tpt) REVERT: T 132 ASN cc_start: 0.8379 (t0) cc_final: 0.8153 (t0) REVERT: U 77 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: U 114 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8038 (tt) REVERT: V 47 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: V 78 ASN cc_start: 0.8282 (m-40) cc_final: 0.8039 (m-40) REVERT: W 47 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7533 (mtp180) REVERT: W 114 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8229 (tt) REVERT: W 294 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8119 (t0) outliers start: 104 outliers final: 57 residues processed: 828 average time/residue: 0.5222 time to fit residues: 709.9154 Evaluate side-chains 718 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 651 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 304 THR 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 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 113 ASP Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 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 L residue 63 VAL Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 230 TYR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 230 TYR Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 376 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 114 LEU Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 294 ASP 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 24 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 555 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 489 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 337 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN K 191 HIS L 26 ASN O 337 GLN Q 389 ASN S 337 GLN W 97 ASN W 164 ASN W 337 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.100830 restraints weight = 97152.652| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.97 r_work: 0.3245 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 51576 Z= 0.261 Angle : 0.614 7.767 70128 Z= 0.313 Chirality : 0.042 0.165 7800 Planarity : 0.005 0.060 9252 Dihedral : 4.170 24.776 7080 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.91 % Allowed : 11.93 % Favored : 85.17 % 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: 2.05 (0.11), residues: 6456 helix: 2.44 (0.09), residues: 3240 sheet: 1.04 (0.24), residues: 456 loop : 0.16 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 348 HIS 0.006 0.001 HIS K 217 PHE 0.019 0.001 PHE C 186 TYR 0.024 0.002 TYR A 230 ARG 0.011 0.001 ARG P 39 *********************** 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 866 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 714 time to evaluate : 4.270 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8605 (mtt) REVERT: A 294 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8284 (t0) REVERT: A 380 MET cc_start: 0.7825 (mmp) cc_final: 0.7549 (mmm) REVERT: B 16 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8572 (tm-30) REVERT: E 18 ARG cc_start: 0.7441 (mmt90) cc_final: 0.7128 (tpp-160) REVERT: E 149 MET cc_start: 0.7215 (mmm) cc_final: 0.6640 (mmm) REVERT: F 27 LYS cc_start: 0.7261 (tptp) cc_final: 0.5779 (mttp) REVERT: G 229 ILE cc_start: 0.8721 (tp) cc_final: 0.8281 (tp) REVERT: G 250 THR cc_start: 0.9420 (m) cc_final: 0.9132 (m) REVERT: G 377 ILE cc_start: 0.7475 (mp) cc_final: 0.7198 (pt) REVERT: H 12 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7607 (tt0) REVERT: H 16 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7742 (tm-30) REVERT: H 20 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7161 (mt-10) REVERT: H 49 ASP cc_start: 0.8161 (m-30) cc_final: 0.7797 (m-30) REVERT: I 67 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8801 (mtp) REVERT: I 222 ASP cc_start: 0.8333 (m-30) cc_final: 0.8111 (m-30) REVERT: I 377 ILE cc_start: 0.7573 (mp) cc_final: 0.7322 (pt) REVERT: L 5 THR cc_start: 0.8384 (p) cc_final: 0.8183 (p) REVERT: L 27 LYS cc_start: 0.7425 (tptp) cc_final: 0.5878 (mttp) REVERT: M 288 MET cc_start: 0.9037 (tpp) cc_final: 0.8550 (tpt) REVERT: O 222 ASP cc_start: 0.8351 (m-30) cc_final: 0.8129 (m-30) REVERT: O 253 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.8028 (mtm110) REVERT: Q 288 MET cc_start: 0.9064 (tpp) cc_final: 0.8711 (tpt) REVERT: S 229 ILE cc_start: 0.8431 (tp) cc_final: 0.8196 (tp) REVERT: T 132 ASN cc_start: 0.8550 (t0) cc_final: 0.8290 (t0) REVERT: U 114 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8311 (tt) REVERT: V 16 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7729 (tt0) REVERT: V 20 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7273 (mt-10) REVERT: V 47 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: W 114 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8446 (tt) outliers start: 152 outliers final: 92 residues processed: 813 average time/residue: 0.5043 time to fit residues: 674.3319 Evaluate side-chains 702 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 604 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 294 ASP 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 47 GLU 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 305 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 34 THR 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 151 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 273 ASP Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 351 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR 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 197 SER Chi-restraints excluded: chain Q residue 390 VAL Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain 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 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 471 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 523 optimal weight: 0.2980 chunk 532 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 chunk 441 optimal weight: 5.9990 chunk 467 optimal weight: 3.9990 chunk 331 optimal weight: 3.9990 chunk 572 optimal weight: 0.0870 chunk 218 optimal weight: 7.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 87 ASN C 169 ASN C 337 GLN E 169 ASN E 276 GLN E 279 GLN F 26 ASN G 169 ASN G 276 GLN G 279 GLN G 337 GLN H 26 ASN L 26 ASN N 26 ASN P 26 ASN Q 382 GLN S 382 GLN S 407 GLN W 97 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099318 restraints weight = 97307.669| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.95 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 51576 Z= 0.247 Angle : 0.568 7.310 70128 Z= 0.291 Chirality : 0.041 0.161 7800 Planarity : 0.005 0.059 9252 Dihedral : 4.149 21.185 7080 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.25 % Allowed : 12.81 % Favored : 83.94 % 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 (0.11), residues: 6456 helix: 2.53 (0.09), residues: 3228 sheet: 0.88 (0.23), residues: 492 loop : 0.18 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 398 HIS 0.015 0.001 HIS U 323 PHE 0.008 0.001 PHE I 285 TYR 0.013 0.001 TYR J 13 ARG 0.009 0.001 ARG I 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 629 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8608 (mtt) REVERT: A 294 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8339 (t0) REVERT: B 16 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 132 ASN cc_start: 0.8055 (t0) cc_final: 0.7777 (t0) REVERT: D 67 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 126 GLN cc_start: 0.6216 (mp10) cc_final: 0.6005 (mp10) REVERT: E 18 ARG cc_start: 0.7595 (mmt90) cc_final: 0.7248 (tpp-160) REVERT: E 54 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: F 27 LYS cc_start: 0.7325 (tptp) cc_final: 0.5636 (mttp) REVERT: G 229 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8364 (tp) REVERT: G 250 THR cc_start: 0.9360 (m) cc_final: 0.9136 (m) REVERT: G 377 ILE cc_start: 0.7532 (mp) cc_final: 0.7246 (pt) REVERT: H 12 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7738 (tt0) REVERT: H 16 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7826 (tm-30) REVERT: H 49 ASP cc_start: 0.8295 (m-30) cc_final: 0.7923 (m-30) REVERT: I 18 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7279 (mtt-85) REVERT: I 377 ILE cc_start: 0.7534 (mp) cc_final: 0.7259 (pt) REVERT: L 126 GLN cc_start: 0.6420 (mp-120) cc_final: 0.6202 (mp10) REVERT: O 222 ASP cc_start: 0.8440 (m-30) cc_final: 0.8199 (m-30) REVERT: Q 288 MET cc_start: 0.8993 (tpp) cc_final: 0.8597 (tpt) REVERT: R 16 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7606 (tt0) REVERT: V 16 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7568 (tt0) REVERT: V 126 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.5721 (mp10) REVERT: W 294 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8360 (t0) REVERT: X 126 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.5628 (mp10) outliers start: 170 outliers final: 113 residues processed: 761 average time/residue: 0.5211 time to fit residues: 647.0220 Evaluate side-chains 712 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 591 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 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 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 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 30 THR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 273 ASP Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 6 ASP Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 22 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 34 GLN Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 208 VAL Chi-restraints excluded: chain W residue 294 ASP Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN 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 223 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 585 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 460 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 169 ASN C 184 GLN E 260 HIS F 26 ASN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN S 389 ASN S 407 GLN W 97 ASN W 164 ASN W 276 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099860 restraints weight = 97072.715| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.95 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51576 Z= 0.193 Angle : 0.535 7.802 70128 Z= 0.273 Chirality : 0.039 0.175 7800 Planarity : 0.004 0.059 9252 Dihedral : 4.005 24.564 7080 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.62 % Allowed : 13.40 % Favored : 83.98 % 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: 2.20 (0.11), residues: 6456 helix: 2.61 (0.09), residues: 3228 sheet: 0.93 (0.23), residues: 492 loop : 0.20 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 398 HIS 0.009 0.001 HIS Q 260 PHE 0.011 0.001 PHE G 186 TYR 0.014 0.001 TYR J 13 ARG 0.015 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 622 time to evaluate : 4.317 Fit side-chains REVERT: A 66 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8822 (m-30) REVERT: B 16 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 132 ASN cc_start: 0.8026 (t0) cc_final: 0.7819 (t0) REVERT: E 18 ARG cc_start: 0.7626 (mmt90) cc_final: 0.7248 (tpp-160) REVERT: E 54 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: E 149 MET cc_start: 0.7396 (mmm) cc_final: 0.7088 (mmm) REVERT: F 27 LYS cc_start: 0.7399 (tptp) cc_final: 0.5651 (mttp) REVERT: F 110 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7794 (mp) REVERT: G 229 ILE cc_start: 0.8666 (tp) cc_final: 0.8296 (tp) REVERT: G 250 THR cc_start: 0.9347 (m) cc_final: 0.9134 (m) REVERT: G 377 ILE cc_start: 0.7511 (mp) cc_final: 0.7218 (pt) REVERT: H 12 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7808 (tt0) REVERT: H 16 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7755 (tm-30) REVERT: H 27 LYS cc_start: 0.7594 (tptp) cc_final: 0.5787 (mttm) REVERT: I 18 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7332 (mtt-85) REVERT: N 15 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8185 (tt0) REVERT: O 222 ASP cc_start: 0.8376 (m-30) cc_final: 0.8155 (m-30) REVERT: O 253 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.8080 (mtm110) REVERT: P 15 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8221 (tt0) REVERT: Q 288 MET cc_start: 0.8964 (tpp) cc_final: 0.8527 (tpt) REVERT: Q 377 ILE cc_start: 0.7758 (mp) cc_final: 0.7523 (mt) REVERT: R 16 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7598 (tt0) REVERT: S 229 ILE cc_start: 0.8453 (tp) cc_final: 0.8144 (tp) REVERT: T 19 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8038 (mtm110) REVERT: V 16 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7669 (tt0) REVERT: V 126 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.5727 (mp10) REVERT: W 66 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: W 294 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (t0) REVERT: X 126 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.5476 (mp10) REVERT: X 131 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7620 (ptt-90) outliers start: 137 outliers final: 91 residues processed: 729 average time/residue: 0.5216 time to fit residues: 627.1642 Evaluate side-chains 684 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 585 time to evaluate : 4.299 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER 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 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 67 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR 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 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 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 376 ASP Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 2 SER 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 R residue 2 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 368 VAL Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 6 ASP 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 279 GLN Chi-restraints excluded: chain W residue 294 ASP Chi-restraints excluded: chain W residue 305 LEU Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 34 optimal weight: 0.7980 chunk 352 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 387 optimal weight: 0.9980 chunk 617 optimal weight: 0.8980 chunk 543 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 573 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN Q 260 HIS Q 389 ASN S 407 GLN U 276 GLN W 260 HIS W 389 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098457 restraints weight = 97269.982| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.94 r_work: 0.3207 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 51576 Z= 0.223 Angle : 0.553 7.229 70128 Z= 0.283 Chirality : 0.040 0.167 7800 Planarity : 0.005 0.065 9252 Dihedral : 4.079 20.610 7080 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.77 % Allowed : 13.61 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.11), residues: 6456 helix: 2.63 (0.09), residues: 3216 sheet: 0.95 (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 0.008 0.001 HIS W 260 PHE 0.010 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.016 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 614 time to evaluate : 4.284 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8875 (m-30) REVERT: B 16 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 107 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8411 (mttm) REVERT: C 54 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: E 18 ARG cc_start: 0.7667 (mmt90) cc_final: 0.7251 (tpp-160) REVERT: E 149 MET cc_start: 0.7383 (mmm) cc_final: 0.7115 (mmm) REVERT: F 27 LYS cc_start: 0.7462 (tptp) cc_final: 0.5711 (mttp) REVERT: G 229 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8335 (tp) REVERT: G 250 THR cc_start: 0.9398 (m) cc_final: 0.9164 (m) REVERT: G 377 ILE cc_start: 0.7575 (mp) cc_final: 0.7206 (pt) REVERT: H 12 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7873 (tt0) REVERT: H 16 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7817 (tm-30) REVERT: H 27 LYS cc_start: 0.7582 (tptp) cc_final: 0.5735 (mttm) REVERT: I 18 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7359 (mtt-85) REVERT: J 132 ASN cc_start: 0.8194 (t0) cc_final: 0.7987 (t0) REVERT: L 112 LEU cc_start: 0.7726 (mm) cc_final: 0.7309 (mt) REVERT: N 15 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8166 (tt0) REVERT: O 222 ASP cc_start: 0.8395 (m-30) cc_final: 0.8167 (m-30) REVERT: O 253 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8074 (mtm110) REVERT: O 377 ILE cc_start: 0.7656 (mp) cc_final: 0.7445 (mt) REVERT: P 15 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8274 (tt0) REVERT: Q 170 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: Q 377 ILE cc_start: 0.7814 (mp) cc_final: 0.7565 (mt) REVERT: R 16 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7720 (tt0) REVERT: S 229 ILE cc_start: 0.8616 (tp) cc_final: 0.8282 (tp) REVERT: T 19 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8073 (mtm110) REVERT: V 16 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7890 (tt0) REVERT: V 126 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.5811 (mp10) REVERT: W 66 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: W 294 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (t0) REVERT: X 126 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.5409 (mp10) outliers start: 145 outliers final: 120 residues processed: 721 average time/residue: 0.5447 time to fit residues: 646.3652 Evaluate side-chains 705 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 577 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 22 SER 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 109 SER Chi-restraints excluded: chain M residue 86 LEU 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 35 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain O residue 376 ASP Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 273 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 R residue 98 LYS 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 T residue 2 SER Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 107 LYS 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 197 SER Chi-restraints excluded: chain W residue 208 VAL Chi-restraints excluded: chain W residue 294 ASP 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 62 SER Chi-restraints excluded: chain X residue 126 GLN Chi-restraints excluded: chain X residue 131 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 146 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 chunk 456 optimal weight: 0.8980 chunk 601 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 630 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 600 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN L 26 ASN N 26 ASN O 260 HIS P 26 ASN R 126 GLN T 126 GLN U 276 GLN U 389 ASN W 164 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098170 restraints weight = 97148.091| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.93 r_work: 0.3205 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51576 Z= 0.217 Angle : 0.548 7.118 70128 Z= 0.280 Chirality : 0.040 0.165 7800 Planarity : 0.005 0.068 9252 Dihedral : 4.055 20.980 7080 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.64 % Allowed : 14.12 % Favored : 83.24 % 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: 2.64 (0.09), residues: 3204 sheet: 0.96 (0.24), residues: 456 loop : 0.15 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 398 HIS 0.004 0.001 HIS O 260 PHE 0.010 0.001 PHE U 274 TYR 0.014 0.001 TYR G 400 ARG 0.015 0.000 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 586 time to evaluate : 4.311 Fit side-chains REVERT: B 16 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 54 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: D 84 LYS cc_start: 0.8710 (mttm) cc_final: 0.8421 (ttmm) REVERT: E 18 ARG cc_start: 0.7674 (mmt90) cc_final: 0.7225 (tpp-160) REVERT: E 54 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: E 149 MET cc_start: 0.7399 (mmm) cc_final: 0.7173 (mmm) REVERT: F 27 LYS cc_start: 0.7462 (tptp) cc_final: 0.5644 (mttp) REVERT: G 229 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8230 (tp) REVERT: G 250 THR cc_start: 0.9396 (m) cc_final: 0.9166 (m) REVERT: G 377 ILE cc_start: 0.7737 (mp) cc_final: 0.7327 (pt) REVERT: H 12 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7892 (tt0) REVERT: H 16 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 27 LYS cc_start: 0.7597 (tptp) cc_final: 0.5747 (mttm) REVERT: I 18 ARG cc_start: 0.7574 (mmt90) cc_final: 0.7371 (mtt-85) REVERT: J 115 ASP cc_start: 0.6502 (p0) cc_final: 0.6217 (p0) REVERT: K 253 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7619 (ttp-110) REVERT: L 112 LEU cc_start: 0.7783 (mm) cc_final: 0.7579 (mt) REVERT: M 362 ARG cc_start: 0.6494 (mmm160) cc_final: 0.6197 (mtm180) REVERT: M 377 ILE cc_start: 0.7888 (mp) cc_final: 0.7567 (pt) REVERT: O 222 ASP cc_start: 0.8403 (m-30) cc_final: 0.8177 (m-30) REVERT: P 15 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8299 (tt0) REVERT: Q 170 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: Q 253 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (ttp-110) REVERT: Q 377 ILE cc_start: 0.7827 (mp) cc_final: 0.7580 (mt) REVERT: R 16 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7652 (tt0) REVERT: S 229 ILE cc_start: 0.8576 (tp) cc_final: 0.8227 (tp) REVERT: T 19 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8083 (mtm110) REVERT: V 16 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7470 (tm-30) REVERT: V 85 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7750 (mm-30) REVERT: V 126 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.5803 (mp10) REVERT: W 66 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (m-30) REVERT: W 294 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8442 (t0) REVERT: X 126 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.5459 (mp10) REVERT: X 131 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7707 (ptt-90) outliers start: 138 outliers final: 109 residues processed: 690 average time/residue: 0.5207 time to fit residues: 586.1361 Evaluate side-chains 693 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 574 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER 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 387 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain M residue 376 ASP Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 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 Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 253 ARG Chi-restraints excluded: chain Q residue 273 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 R residue 98 LYS 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 T residue 2 SER Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 25 VAL 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 294 ASP 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 25 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN 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 98 optimal weight: 3.9990 chunk 566 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 626 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 381 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 489 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 412 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN I 260 HIS ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 HIS L 26 ASN N 26 ASN P 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098316 restraints weight = 97434.249| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.93 r_work: 0.3206 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7761 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= 0.206 Angle : 0.542 7.870 70128 Z= 0.277 Chirality : 0.039 0.159 7800 Planarity : 0.005 0.072 9252 Dihedral : 4.029 20.158 7080 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.52 % Allowed : 14.30 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.11), residues: 6456 helix: 2.67 (0.09), residues: 3204 sheet: 0.95 (0.24), residues: 456 loop : 0.13 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 398 HIS 0.008 0.001 HIS K 260 PHE 0.009 0.001 PHE G 186 TYR 0.013 0.001 TYR T 90 ARG 0.017 0.000 ARG I 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 721 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 589 time to evaluate : 4.338 Fit side-chains REVERT: B 16 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 85 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 107 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8414 (mttm) REVERT: C 54 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: D 84 LYS cc_start: 0.8721 (mttm) cc_final: 0.8437 (ttmm) REVERT: E 18 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7197 (tpp-160) REVERT: E 54 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: E 149 MET cc_start: 0.7385 (mmm) cc_final: 0.7168 (mmm) REVERT: F 27 LYS cc_start: 0.7450 (tptp) cc_final: 0.5618 (mttp) REVERT: F 126 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5359 (mp10) REVERT: G 229 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (tp) REVERT: G 250 THR cc_start: 0.9409 (m) cc_final: 0.9170 (m) REVERT: H 12 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7895 (tt0) REVERT: H 16 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7845 (tm-30) REVERT: H 27 LYS cc_start: 0.7635 (tptp) cc_final: 0.5770 (mttm) REVERT: H 126 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.5376 (mp10) REVERT: J 115 ASP cc_start: 0.6311 (p0) cc_final: 0.6067 (p0) REVERT: K 253 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7649 (ttp-110) REVERT: L 112 LEU cc_start: 0.7788 (mm) cc_final: 0.7588 (mt) REVERT: M 362 ARG cc_start: 0.6458 (mmm160) cc_final: 0.6216 (mtm180) REVERT: M 377 ILE cc_start: 0.7879 (mp) cc_final: 0.7518 (pt) REVERT: O 222 ASP cc_start: 0.8378 (m-30) cc_final: 0.8168 (m-30) REVERT: O 253 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7822 (ttp-110) REVERT: P 15 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8311 (tt0) REVERT: Q 170 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: Q 253 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7766 (ttp-110) REVERT: Q 377 ILE cc_start: 0.7846 (mp) cc_final: 0.7597 (mt) REVERT: R 16 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7674 (tt0) REVERT: S 229 ILE cc_start: 0.8572 (tp) cc_final: 0.8204 (tp) REVERT: T 19 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8082 (mtm110) REVERT: T 85 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7829 (mm-30) REVERT: V 126 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.5872 (mp10) REVERT: W 294 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8401 (t0) REVERT: X 126 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.5485 (mp10) REVERT: X 131 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7936 (ptt-90) outliers start: 132 outliers final: 115 residues processed: 688 average time/residue: 0.5249 time to fit residues: 587.1847 Evaluate side-chains 692 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 567 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 THR Chi-restraints excluded: chain K residue 297 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain L residue 2 SER 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 109 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 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 35 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 273 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 R residue 98 LYS 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 T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain V residue 126 GLN Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 208 VAL Chi-restraints excluded: chain W residue 294 ASP 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 25 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN 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 430 optimal weight: 6.9990 chunk 534 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 398 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 606 optimal weight: 0.7980 chunk 450 optimal weight: 0.9980 chunk 545 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 468 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 407 GLN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 26 ASN P 26 ASN U 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098466 restraints weight = 97421.904| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.93 r_work: 0.3208 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.7856 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= 0.196 Angle : 0.537 8.336 70128 Z= 0.274 Chirality : 0.039 0.158 7800 Planarity : 0.005 0.073 9252 Dihedral : 3.981 19.788 7080 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.39 % Allowed : 14.41 % 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: 2.22 (0.11), residues: 6456 helix: 2.69 (0.09), residues: 3204 sheet: 1.00 (0.24), residues: 456 loop : 0.14 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 398 HIS 0.003 0.001 HIS K 217 PHE 0.009 0.001 PHE G 186 TYR 0.013 0.001 TYR J 13 ARG 0.017 0.000 ARG G 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12912 Ramachandran restraints generated. 6456 Oldfield, 0 Emsley, 6456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 576 time to evaluate : 4.334 Fit side-chains REVERT: B 16 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 107 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8393 (mttm) REVERT: C 54 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: D 84 LYS cc_start: 0.8778 (mttm) cc_final: 0.8465 (ttmm) REVERT: E 18 ARG cc_start: 0.7694 (mmt90) cc_final: 0.7273 (tpp-160) REVERT: E 54 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: E 149 MET cc_start: 0.7351 (mmm) cc_final: 0.7135 (mmm) REVERT: F 27 LYS cc_start: 0.7476 (tptp) cc_final: 0.5623 (mttp) REVERT: F 126 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.5338 (mp10) REVERT: G 229 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8177 (tp) REVERT: H 12 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7900 (tt0) REVERT: H 27 LYS cc_start: 0.7636 (tptp) cc_final: 0.5778 (mttm) REVERT: H 126 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5310 (mp10) REVERT: J 115 ASP cc_start: 0.6524 (p0) cc_final: 0.6294 (p0) REVERT: K 362 ARG cc_start: 0.6678 (mmm160) cc_final: 0.6398 (ttm-80) REVERT: M 377 ILE cc_start: 0.7904 (mp) cc_final: 0.7503 (pt) REVERT: O 222 ASP cc_start: 0.8356 (m-30) cc_final: 0.8138 (m-30) REVERT: O 253 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7860 (ttp-110) REVERT: P 15 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8309 (tt0) REVERT: P 132 ASN cc_start: 0.8554 (t0) cc_final: 0.8160 (t0) REVERT: Q 170 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: Q 253 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7793 (ttp-110) REVERT: Q 377 ILE cc_start: 0.7859 (mp) cc_final: 0.7611 (mt) REVERT: R 16 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7674 (tt0) REVERT: S 229 ILE cc_start: 0.8549 (tp) cc_final: 0.8173 (tp) REVERT: S 279 GLN cc_start: 0.5601 (mm110) cc_final: 0.5342 (mp10) REVERT: T 19 ARG cc_start: 0.8328 (ttp80) cc_final: 0.8088 (mtm110) REVERT: V 85 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7612 (mm-30) REVERT: W 294 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8417 (t0) REVERT: X 126 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.5536 (mp10) REVERT: X 131 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7687 (ptt-90) outliers start: 125 outliers final: 110 residues processed: 675 average time/residue: 0.5297 time to fit residues: 580.3641 Evaluate side-chains 676 residues out of total 5232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 556 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain 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 K residue 343 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 197 SER Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 304 THR Chi-restraints excluded: chain O residue 351 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain Q residue 6 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 253 ARG Chi-restraints excluded: chain Q residue 273 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 R residue 98 LYS 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 T residue 2 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 197 SER Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain V residue 2 SER Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 112 LEU Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 197 SER Chi-restraints excluded: chain W residue 208 VAL Chi-restraints excluded: chain W residue 294 ASP 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 25 VAL Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 126 GLN 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 425 optimal weight: 0.0870 chunk 487 optimal weight: 5.9990 chunk 393 optimal weight: 0.0270 chunk 269 optimal weight: 0.9990 chunk 360 optimal weight: 0.2980 chunk 354 optimal weight: 1.9990 chunk 607 optimal weight: 0.7980 chunk 498 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN M 110 HIS N 26 ASN P 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100544 restraints weight = 97244.062| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.93 r_work: 0.3246 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 51576 Z= 0.149 Angle : 0.509 8.298 70128 Z= 0.260 Chirality : 0.038 0.153 7800 Planarity : 0.004 0.072 9252 Dihedral : 3.804 18.900 7080 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 14.98 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.11), residues: 6456 helix: 2.72 (0.09), residues: 3228 sheet: 1.01 (0.23), residues: 492 loop : 0.18 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 211 HIS 0.002 0.000 HIS I 323 PHE 0.009 0.001 PHE A 369 TYR 0.012 0.001 TYR J 13 ARG 0.017 0.000 ARG G 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23030.51 seconds wall clock time: 395 minutes 45.45 seconds (23745.45 seconds total)