Starting phenix.real_space_refine on Sun Aug 9 21:00:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.map" model { file = "/net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l5i_62834/08_2026/9l5i_62834.cif" } resolution = 1.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.017 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 216 5.16 5 C 23008 2.51 5 N 6096 2.21 5 O 8780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38100 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3385 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 422, 3308 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 422, 3308 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 4 bond proxies already assigned to first conformer: 3297 Chain: "S" Number of atoms: 1082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 123, 1027 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 123, 1024 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} bond proxies already assigned to first conformer: 994 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "S" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "H" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "I" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "J" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "K" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "L" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "M" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "N" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Classifications: {'water': 207} Link IDs: {None: 206} Chain: "O" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Restraints were copied for chains: B, D, F, H, J, L, N, C, E, G, I, K, M, O Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N ACYS A 247 " occ=0.67 ... (10 atoms not shown) pdb=" SG BCYS A 247 " occ=0.33 residue: pdb=" N APHE A 402 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 402 " occ=0.50 residue group: pdb=" N AGLN S 2 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS S 2 " occ=0.50 residue group: pdb=" N ATHR S 22 " occ=0.50 ... (11 atoms not shown) pdb=" OG BSER S 22 " occ=0.50 residue group: pdb=" N ASER S 24 " occ=0.50 ... (11 atoms not shown) pdb=" CG2BVAL S 24 " occ=0.50 residue group: pdb=" N AILE S 34 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU S 34 " occ=0.50 residue group: pdb=" N ASER S 58 " occ=0.50 ... (11 atoms not shown) pdb=" CG2BTHR S 58 " occ=0.50 residue group: pdb=" N AASN S 96 " occ=0.50 ... (10 atoms not shown) pdb=" O BGLY S 96 " occ=0.50 residue: pdb=" N ACYS B 247 " occ=0.67 ... (10 atoms not shown) pdb=" SG BCYS B 247 " occ=0.33 residue: pdb=" N APHE B 402 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 402 " occ=0.50 residue group: pdb=" N AGLN C 2 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 2 " occ=0.50 residue group: pdb=" N ATHR C 22 " occ=0.50 ... (11 atoms not shown) pdb=" OG BSER C 22 " occ=0.50 ... (remaining 60 not shown) Time building chain proxies: 6.62, per 1000 atoms: 0.17 Number of scatterers: 38100 At special positions: 0 Unit cell: (129.63, 129.63, 124.41, 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 216 16.00 O 8780 8.00 N 6096 7.00 C 23008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG ACYS A 247 " - pdb=" SG ACYS H 247 " distance=2.05 Simple disulfide: pdb=" SG ACYS B 247 " - pdb=" SG ACYS J 247 " distance=2.05 Simple disulfide: pdb=" SG ACYS D 247 " - pdb=" SG ACYS N 247 " distance=2.05 Simple disulfide: pdb=" SG ACYS F 247 " - pdb=" SG ACYS L 247 " distance=2.05 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: 3.12 Conformation dependent library (CDL) restraints added in 2.5 seconds 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 32 sheets defined 47.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 36 Processing helix chain 'S' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL S 83 " --> pdb=" O ASP S 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY B 64 " --> pdb=" O SER B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY D 64 " --> pdb=" O SER D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY F 64 " --> pdb=" O SER F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 Processing helix chain 'H' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY H 64 " --> pdb=" O SER H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 65 through 70 Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 450 " --> pdb=" O ARG H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL I 83 " --> pdb=" O ASP I 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 Processing helix chain 'J' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY J 64 " --> pdb=" O SER J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 65 through 70 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 154 through 163 Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY J 195 " --> pdb=" O GLU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 246 through 261 Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 273 through 288 Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE J 301 " --> pdb=" O MET J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU J 314 " --> pdb=" O HIS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 351 Processing helix chain 'J' and resid 357 through 361 Processing helix chain 'J' and resid 383 through 385 No H-bonds generated for 'chain 'J' and resid 383 through 385' Processing helix chain 'J' and resid 386 through 395 Processing helix chain 'J' and resid 412 through 433 Processing helix chain 'J' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN J 442 " --> pdb=" O ALA J 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU J 443 " --> pdb=" O VAL J 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 450 " --> pdb=" O ARG J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL J 461 " --> pdb=" O ALA J 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 60 Processing helix chain 'L' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY L 64 " --> pdb=" O SER L 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 61 through 64' Processing helix chain 'L' and resid 65 through 70 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 122 Processing helix chain 'L' and resid 123 through 127 Processing helix chain 'L' and resid 141 through 146 Processing helix chain 'L' and resid 154 through 163 Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY L 195 " --> pdb=" O GLU L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 246 through 261 Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 273 through 288 Processing helix chain 'L' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE L 301 " --> pdb=" O MET L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU L 314 " --> pdb=" O HIS L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 351 Processing helix chain 'L' and resid 357 through 361 Processing helix chain 'L' and resid 383 through 385 No H-bonds generated for 'chain 'L' and resid 383 through 385' Processing helix chain 'L' and resid 386 through 395 Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN L 442 " --> pdb=" O ALA L 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU L 443 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS L 450 " --> pdb=" O ARG L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL L 461 " --> pdb=" O ALA L 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL M 83 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 60 Processing helix chain 'N' and resid 61 through 64 removed outlier: 6.017A pdb=" N GLY N 64 " --> pdb=" O SER N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 65 through 70 Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 112 through 122 Processing helix chain 'N' and resid 123 through 127 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 154 through 163 Processing helix chain 'N' and resid 181 through 195 removed outlier: 3.504A pdb=" N GLY N 195 " --> pdb=" O GLU N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 233 Processing helix chain 'N' and resid 246 through 261 Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 273 through 288 Processing helix chain 'N' and resid 297 through 303 removed outlier: 3.912A pdb=" N ILE N 301 " --> pdb=" O MET N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 322 removed outlier: 3.606A pdb=" N LEU N 314 " --> pdb=" O HIS N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 351 Processing helix chain 'N' and resid 357 through 361 Processing helix chain 'N' and resid 383 through 385 No H-bonds generated for 'chain 'N' and resid 383 through 385' Processing helix chain 'N' and resid 386 through 395 Processing helix chain 'N' and resid 412 through 433 Processing helix chain 'N' and resid 436 through 450 removed outlier: 6.739A pdb=" N ASN N 442 " --> pdb=" O ALA N 438 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU N 443 " --> pdb=" O VAL N 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS N 450 " --> pdb=" O ARG N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 462 removed outlier: 3.705A pdb=" N VAL N 461 " --> pdb=" O ALA N 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 79 through 94 removed outlier: 4.111A pdb=" N VAL O 83 " --> pdb=" O ASP O 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP A 202 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS A 294 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY A 171 " --> pdb=" O APHE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'S' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL S 42 " --> pdb=" O TRP S 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE S 99 " --> pdb=" O ALA S 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP B 202 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY B 171 " --> pdb=" O APHE B 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA8, first strand: chain 'C' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL C 42 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 99 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP D 202 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN D 401 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA D 378 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY D 171 " --> pdb=" O APHE D 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'E' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL E 42 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 99 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP F 202 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS F 294 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY F 171 " --> pdb=" O APHE F 402 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL G 42 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE G 99 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP H 202 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS H 294 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY H 171 " --> pdb=" O APHE H 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'I' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL I 42 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE I 99 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS J 86 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU J 37 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU J 138 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA J 39 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP J 202 " --> pdb=" O ASN J 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS J 294 " --> pdb=" O VAL J 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE J 326 " --> pdb=" O VAL J 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE J 402 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY J 171 " --> pdb=" O APHE J 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'K' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL K 42 " --> pdb=" O TRP K 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE K 99 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS L 84 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA L 102 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS L 86 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU L 37 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU L 138 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA L 39 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR L 200 " --> pdb=" O TYR L 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN L 241 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP L 202 " --> pdb=" O ASN L 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS L 238 " --> pdb=" O ILE L 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET L 266 " --> pdb=" O HIS L 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU L 240 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP L 268 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL L 265 " --> pdb=" O HIS L 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS L 294 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS L 267 " --> pdb=" O HIS L 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE L 326 " --> pdb=" O VAL L 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN L 401 " --> pdb=" O PRO L 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA L 378 " --> pdb=" O GLN L 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU L 169 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE L 402 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY L 171 " --> pdb=" O APHE L 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'M' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL M 42 " --> pdb=" O TRP M 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE M 99 " --> pdb=" O ALA M 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 83 through 88 removed outlier: 5.685A pdb=" N CYS N 84 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA N 102 " --> pdb=" O CYS N 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS N 86 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU N 37 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU N 138 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA N 39 " --> pdb=" O GLU N 136 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 169 through 174 removed outlier: 7.158A pdb=" N THR N 200 " --> pdb=" O TYR N 239 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN N 241 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASP N 202 " --> pdb=" O ASN N 241 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N HIS N 238 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET N 266 " --> pdb=" O HIS N 238 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU N 240 " --> pdb=" O MET N 266 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ASP N 268 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL N 265 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS N 294 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS N 267 " --> pdb=" O HIS N 294 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE N 326 " --> pdb=" O VAL N 377 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN N 401 " --> pdb=" O PRO N 376 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA N 378 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU N 169 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N APHE N 402 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY N 171 " --> pdb=" O APHE N 402 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 353 through 354 Processing sheet with id=AD5, first strand: chain 'O' and resid 68 through 70 removed outlier: 4.592A pdb=" N VAL O 42 " --> pdb=" O TRP O 70 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE O 99 " --> pdb=" O ALA O 117 " (cutoff:3.500A) 1664 hydrogen bonds defined for protein. 4592 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: 8.78 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7664 1.33 - 1.45: 10176 1.45 - 1.57: 18744 1.57 - 1.69: 0 1.69 - 1.81: 296 Bond restraints: 36880 Sorted by residual: bond pdb=" C GLY L 308 " pdb=" O GLY L 308 " ideal model delta sigma weight residual 1.236 1.218 0.018 5.30e-03 3.56e+04 1.19e+01 bond pdb=" C GLY N 308 " pdb=" O GLY N 308 " ideal model delta sigma weight residual 1.236 1.218 0.018 5.30e-03 3.56e+04 1.19e+01 bond pdb=" C GLY B 308 " pdb=" O GLY B 308 " ideal model delta sigma weight residual 1.236 1.218 0.018 5.30e-03 3.56e+04 1.19e+01 bond pdb=" C GLY J 308 " pdb=" O GLY J 308 " ideal model delta sigma weight residual 1.236 1.218 0.018 5.30e-03 3.56e+04 1.19e+01 bond pdb=" C GLY A 308 " pdb=" O GLY A 308 " ideal model delta sigma weight residual 1.236 1.218 0.018 5.30e-03 3.56e+04 1.19e+01 ... (remaining 36875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 47664 3.02 - 6.05: 2464 6.05 - 9.07: 152 9.07 - 12.09: 8 12.09 - 15.11: 8 Bond angle restraints: 50296 Sorted by residual: angle pdb=" CG MET N 387 " pdb=" SD MET N 387 " pdb=" CE MET N 387 " ideal model delta sigma weight residual 100.90 85.79 15.11 2.20e+00 2.07e-01 4.72e+01 angle pdb=" CG MET J 387 " pdb=" SD MET J 387 " pdb=" CE MET J 387 " ideal model delta sigma weight residual 100.90 85.79 15.11 2.20e+00 2.07e-01 4.72e+01 angle pdb=" CG MET L 387 " pdb=" SD MET L 387 " pdb=" CE MET L 387 " ideal model delta sigma weight residual 100.90 85.79 15.11 2.20e+00 2.07e-01 4.72e+01 angle pdb=" CG MET H 387 " pdb=" SD MET H 387 " pdb=" CE MET H 387 " ideal model delta sigma weight residual 100.90 85.79 15.11 2.20e+00 2.07e-01 4.72e+01 angle pdb=" CG MET F 387 " pdb=" SD MET F 387 " pdb=" CE MET F 387 " ideal model delta sigma weight residual 100.90 85.79 15.11 2.20e+00 2.07e-01 4.72e+01 ... (remaining 50291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 20096 16.06 - 32.12: 1400 32.12 - 48.19: 296 48.19 - 64.25: 108 64.25 - 80.31: 72 Dihedral angle restraints: 21972 sinusoidal: 8764 harmonic: 13208 Sorted by residual: dihedral pdb=" CB ACYS A 247 " pdb=" SG ACYS A 247 " pdb=" SG ACYS H 247 " pdb=" CB ACYS H 247 " ideal model delta sinusoidal sigma weight residual -86.00 -34.53 -51.47 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CB ACYS D 247 " pdb=" SG ACYS D 247 " pdb=" SG ACYS N 247 " pdb=" CB ACYS N 247 " ideal model delta sinusoidal sigma weight residual -86.00 -34.53 -51.47 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CB ACYS B 247 " pdb=" SG ACYS B 247 " pdb=" SG ACYS J 247 " pdb=" CB ACYS J 247 " ideal model delta sinusoidal sigma weight residual -86.00 -34.53 -51.47 1 1.00e+01 1.00e-02 3.62e+01 ... (remaining 21969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2480 0.051 - 0.102: 1832 0.102 - 0.153: 824 0.153 - 0.204: 208 0.204 - 0.255: 40 Chirality restraints: 5384 Sorted by residual: chirality pdb=" CA TYR D 269 " pdb=" N TYR D 269 " pdb=" C TYR D 269 " pdb=" CB TYR D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA TYR L 269 " pdb=" N TYR L 269 " pdb=" C TYR L 269 " pdb=" CB TYR L 269 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA TYR N 269 " pdb=" N TYR N 269 " pdb=" C TYR N 269 " pdb=" CB TYR N 269 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 5381 not shown) Planarity restraints: 6520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 283 " 0.067 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR H 283 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 283 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR H 283 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 283 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 283 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 283 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 283 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 283 " 0.067 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR L 283 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR L 283 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 283 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR L 283 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR L 283 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR L 283 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR L 283 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 283 " 0.067 2.00e-02 2.50e+03 3.48e-02 2.42e+01 pdb=" CG TYR B 283 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 283 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 283 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 283 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 283 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 283 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 283 " 0.044 2.00e-02 2.50e+03 ... (remaining 6517 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 2196 2.66 - 3.22: 39708 3.22 - 3.78: 76440 3.78 - 4.34: 109272 4.34 - 4.90: 164748 Nonbonded interactions: 392364 Sorted by model distance: nonbonded pdb=" SD MET N 212 " pdb=" O HOH N 805 " model vdw 2.102 3.400 nonbonded pdb=" SD MET D 212 " pdb=" O HOH D 803 " model vdw 2.102 3.400 nonbonded pdb=" SD MET J 212 " pdb=" O HOH J 804 " model vdw 2.102 3.400 nonbonded pdb=" SD MET B 212 " pdb=" O HOH B 802 " model vdw 2.102 3.400 nonbonded pdb=" SD MET A 212 " pdb=" O HOH A 803 " model vdw 2.102 3.400 ... (remaining 392359 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'S' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.27 max=1.00 mean=0.97 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: 1.070 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.370 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.010 0.066 36884 Z= 0.608 Angle : 1.502 15.114 50304 Z= 0.979 Chirality : 0.079 0.255 5384 Planarity : 0.014 0.184 6520 Dihedral : 13.185 80.309 13624 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.63 % Allowed : 3.57 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.11), residues: 4560 helix: 0.11 (0.10), residues: 1832 sheet: -0.82 (0.16), residues: 744 loop : -0.61 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG L 360 TYR 0.067 0.011 TYR L 283 PHE 0.029 0.008 PHE E 50 TRP 0.028 0.009 TRP A 70 HIS 0.021 0.005 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.61 (36880) covalent geometry : angle 1.49619 / 0.98 (50296) SS BOND : bond 0.01422 / 0.71 ( 4) SS BOND : angle 10.22566 / 6.42 ( 8) hydrogen bonds : bond 0.14311 / 9.14 ( 1664) hydrogen bonds : angle 8.27902 / 5.95 ( 4592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 517 time to evaluate : 1.611 Fit side-chains REVERT: A 212 MET cc_start: 0.6828 (ttm) cc_final: 0.6432 (ttp) REVERT: A 250 MET cc_start: 0.6906 (ttp) cc_final: 0.6512 (ttp) REVERT: A 305 LYS cc_start: 0.6053 (mmmt) cc_final: 0.5619 (mmmt) REVERT: A 309 MET cc_start: 0.6442 (mtp) cc_final: 0.6199 (mtm) REVERT: A 356 LYS cc_start: 0.6765 (ttpm) cc_final: 0.5877 (tttt) REVERT: A 387 MET cc_start: 0.6733 (mmt) cc_final: 0.6525 (mmt) REVERT: A 440 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5916 (mt-10) REVERT: A 443 GLU cc_start: 0.5813 (mm-30) cc_final: 0.4936 (mp0) REVERT: S 1 MET cc_start: 0.7709 (ttm) cc_final: 0.7382 (ttp) REVERT: S 37 LYS cc_start: 0.5970 (mmtp) cc_final: 0.5768 (mmtm) REVERT: S 47 GLU cc_start: 0.5715 (mm-30) cc_final: 0.5218 (mt-10) REVERT: B 212 MET cc_start: 0.6825 (ttm) cc_final: 0.6430 (ttp) REVERT: B 250 MET cc_start: 0.6912 (ttp) cc_final: 0.6517 (ttp) REVERT: B 305 LYS cc_start: 0.6037 (mmmt) cc_final: 0.5600 (mmmt) REVERT: B 309 MET cc_start: 0.6430 (mtp) cc_final: 0.6187 (mtm) REVERT: B 356 LYS cc_start: 0.6805 (ttpm) cc_final: 0.5915 (tttt) REVERT: B 387 MET cc_start: 0.6724 (mmt) cc_final: 0.6519 (mmt) REVERT: B 440 GLU cc_start: 0.6283 (mt-10) cc_final: 0.5862 (mt-10) REVERT: B 443 GLU cc_start: 0.5798 (mm-30) cc_final: 0.4920 (mp0) REVERT: C 1 MET cc_start: 0.7746 (ttm) cc_final: 0.7418 (ttp) REVERT: C 37 LYS cc_start: 0.5955 (mmtp) cc_final: 0.5753 (mmtm) REVERT: C 47 GLU cc_start: 0.5703 (mm-30) cc_final: 0.5206 (mt-10) REVERT: C 92 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5854 (tttp) REVERT: D 212 MET cc_start: 0.6833 (ttm) cc_final: 0.6438 (ttp) REVERT: D 250 MET cc_start: 0.6918 (ttp) cc_final: 0.6521 (ttp) REVERT: D 305 LYS cc_start: 0.6094 (mmmt) cc_final: 0.5669 (mmmt) REVERT: D 309 MET cc_start: 0.6408 (mtp) cc_final: 0.6169 (mtm) REVERT: D 356 LYS cc_start: 0.6763 (ttpm) cc_final: 0.5877 (tttt) REVERT: D 387 MET cc_start: 0.6686 (mmt) cc_final: 0.6479 (mmt) REVERT: D 440 GLU cc_start: 0.6319 (mt-10) cc_final: 0.5895 (mt-10) REVERT: D 443 GLU cc_start: 0.5834 (mm-30) cc_final: 0.4967 (mp0) REVERT: E 1 MET cc_start: 0.7712 (ttm) cc_final: 0.7383 (ttp) REVERT: E 37 LYS cc_start: 0.5925 (mmtp) cc_final: 0.5725 (mmtm) REVERT: E 47 GLU cc_start: 0.5708 (mm-30) cc_final: 0.5211 (mt-10) REVERT: E 92 LYS cc_start: 0.6184 (ttpp) cc_final: 0.5825 (tttp) REVERT: F 212 MET cc_start: 0.6832 (ttm) cc_final: 0.6441 (ttp) REVERT: F 250 MET cc_start: 0.6892 (ttp) cc_final: 0.6498 (ttp) REVERT: F 305 LYS cc_start: 0.6086 (mmmt) cc_final: 0.5661 (mmmt) REVERT: F 309 MET cc_start: 0.6437 (mtp) cc_final: 0.6195 (mtm) REVERT: F 387 MET cc_start: 0.6713 (mmt) cc_final: 0.6507 (mmt) REVERT: F 440 GLU cc_start: 0.6403 (mt-10) cc_final: 0.5980 (mt-10) REVERT: F 443 GLU cc_start: 0.5861 (mm-30) cc_final: 0.4991 (mp0) REVERT: G 1 MET cc_start: 0.7661 (ttm) cc_final: 0.7333 (ttp) REVERT: G 37 LYS cc_start: 0.5931 (mmtp) cc_final: 0.5730 (mmtm) REVERT: G 47 GLU cc_start: 0.5721 (mm-30) cc_final: 0.5222 (mt-10) REVERT: G 92 LYS cc_start: 0.6169 (ttpp) cc_final: 0.5813 (tttp) REVERT: H 123 ASN cc_start: 0.4321 (m-40) cc_final: 0.4004 (t0) REVERT: H 175 LYS cc_start: 0.5204 (ttmt) cc_final: 0.4865 (ttmm) REVERT: H 212 MET cc_start: 0.6827 (ttm) cc_final: 0.6436 (ttp) REVERT: H 250 MET cc_start: 0.6898 (ttp) cc_final: 0.6508 (ttp) REVERT: H 305 LYS cc_start: 0.6033 (mmmt) cc_final: 0.5604 (mmmt) REVERT: H 309 MET cc_start: 0.6427 (mtp) cc_final: 0.6188 (mtm) REVERT: H 356 LYS cc_start: 0.6763 (ttpm) cc_final: 0.5875 (tttt) REVERT: H 387 MET cc_start: 0.6759 (mmt) cc_final: 0.6552 (mmt) REVERT: H 440 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5953 (mt-10) REVERT: H 443 GLU cc_start: 0.5847 (mm-30) cc_final: 0.4963 (mp0) REVERT: I 1 MET cc_start: 0.7747 (ttm) cc_final: 0.7424 (ttp) REVERT: I 37 LYS cc_start: 0.6009 (mmtp) cc_final: 0.5804 (mmtm) REVERT: I 47 GLU cc_start: 0.5769 (mm-30) cc_final: 0.5277 (mt-10) REVERT: J 123 ASN cc_start: 0.4330 (m-40) cc_final: 0.4011 (t0) REVERT: J 212 MET cc_start: 0.6821 (ttm) cc_final: 0.6426 (ttp) REVERT: J 250 MET cc_start: 0.6898 (ttp) cc_final: 0.6506 (ttp) REVERT: J 305 LYS cc_start: 0.6018 (mmmt) cc_final: 0.5589 (mmmt) REVERT: J 309 MET cc_start: 0.6387 (mtp) cc_final: 0.6146 (mtm) REVERT: J 356 LYS cc_start: 0.6684 (ttpm) cc_final: 0.5794 (tttt) REVERT: J 387 MET cc_start: 0.6784 (mmt) cc_final: 0.6574 (mmt) REVERT: J 440 GLU cc_start: 0.6431 (mt-10) cc_final: 0.6002 (mt-10) REVERT: J 443 GLU cc_start: 0.5849 (mm-30) cc_final: 0.4963 (mp0) REVERT: K 1 MET cc_start: 0.7708 (ttm) cc_final: 0.7380 (ttp) REVERT: K 37 LYS cc_start: 0.6037 (mmtp) cc_final: 0.5833 (mmtm) REVERT: K 47 GLU cc_start: 0.5809 (mm-30) cc_final: 0.5316 (mt-10) REVERT: L 212 MET cc_start: 0.6836 (ttm) cc_final: 0.6439 (ttp) REVERT: L 250 MET cc_start: 0.6897 (ttp) cc_final: 0.6505 (ttp) REVERT: L 305 LYS cc_start: 0.6073 (mmmt) cc_final: 0.5646 (mmmt) REVERT: L 309 MET cc_start: 0.6414 (mtp) cc_final: 0.6175 (mtm) REVERT: L 356 LYS cc_start: 0.6763 (ttpm) cc_final: 0.5881 (tttt) REVERT: L 387 MET cc_start: 0.6730 (mmt) cc_final: 0.6525 (mmt) REVERT: L 440 GLU cc_start: 0.6401 (mt-10) cc_final: 0.5974 (mt-10) REVERT: L 443 GLU cc_start: 0.5873 (mm-30) cc_final: 0.4999 (mp0) REVERT: M 1 MET cc_start: 0.7729 (ttm) cc_final: 0.7404 (ttp) REVERT: M 37 LYS cc_start: 0.5937 (mmtp) cc_final: 0.5735 (mmtm) REVERT: M 47 GLU cc_start: 0.5770 (mm-30) cc_final: 0.5281 (mt-10) REVERT: N 212 MET cc_start: 0.6825 (ttm) cc_final: 0.6427 (ttp) REVERT: N 250 MET cc_start: 0.6923 (ttp) cc_final: 0.6528 (ttp) REVERT: N 305 LYS cc_start: 0.6084 (mmmt) cc_final: 0.5654 (mmmt) REVERT: N 309 MET cc_start: 0.6445 (mtp) cc_final: 0.6201 (mtm) REVERT: N 356 LYS cc_start: 0.6727 (ttpm) cc_final: 0.5844 (tttt) REVERT: N 387 MET cc_start: 0.6728 (mmt) cc_final: 0.6518 (mmt) REVERT: N 440 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5977 (mt-10) REVERT: N 443 GLU cc_start: 0.5862 (mm-30) cc_final: 0.4985 (mp0) REVERT: O 1 MET cc_start: 0.7678 (ttm) cc_final: 0.7352 (ttp) REVERT: O 37 LYS cc_start: 0.5963 (mmtp) cc_final: 0.5761 (mmtm) REVERT: O 47 GLU cc_start: 0.5816 (mm-30) cc_final: 0.5324 (mt-10) REVERT: O 92 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5716 (tttp) outliers start: 8 outliers final: 0 residues processed: 525 average time/residue: 0.8998 time to fit residues: 557.6978 Evaluate side-chains 485 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN B 123 ASN D 123 ASN F 123 ASN L 123 ASN N 123 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.164800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.131094 restraints weight = 130517.752| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.26 r_work: 0.3026 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.2856 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36884 Z= 0.169 Angle : 0.658 6.715 50304 Z= 0.350 Chirality : 0.045 0.157 5384 Planarity : 0.005 0.039 6520 Dihedral : 5.450 21.480 5136 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.42 % Allowed : 4.60 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 4560 helix: 1.83 (0.12), residues: 1792 sheet: -0.82 (0.17), residues: 712 loop : -0.01 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 167 TYR 0.019 0.002 TYR A 24 PHE 0.032 0.002 PHE D 345 TRP 0.021 0.002 TRP N 70 HIS 0.009 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (36880) covalent geometry : angle 0.65625 / 0.35 (50296) SS BOND : bond 0.01172 / 0.59 ( 4) SS BOND : angle 3.87748 / 2.43 ( 8) hydrogen bonds : bond 0.04903 / 3.20 ( 1664) hydrogen bonds : angle 6.75731 / 4.90 ( 4592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.337 Fit side-chains REVERT: A 250 MET cc_start: 0.9124 (ttp) cc_final: 0.8481 (ttp) REVERT: A 252 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8521 (mmtm) REVERT: A 356 LYS cc_start: 0.8842 (ttpm) cc_final: 0.8465 (tttt) REVERT: S 1 MET cc_start: 0.8661 (ttm) cc_final: 0.8437 (ttp) REVERT: S 89 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8250 (tt0) REVERT: B 250 MET cc_start: 0.9128 (ttp) cc_final: 0.8485 (ttp) REVERT: B 252 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8507 (mmtm) REVERT: B 356 LYS cc_start: 0.8844 (ttpm) cc_final: 0.8473 (tttt) REVERT: C 1 MET cc_start: 0.8674 (ttm) cc_final: 0.8443 (ttp) REVERT: C 89 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8259 (tt0) REVERT: C 93 GLU cc_start: 0.8642 (tt0) cc_final: 0.8402 (tt0) REVERT: D 250 MET cc_start: 0.9125 (ttp) cc_final: 0.8479 (ttp) REVERT: D 252 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8492 (mmtm) REVERT: D 356 LYS cc_start: 0.8843 (ttpm) cc_final: 0.8472 (tttt) REVERT: E 1 MET cc_start: 0.8645 (ttm) cc_final: 0.8414 (ttp) REVERT: E 89 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8264 (tt0) REVERT: E 93 GLU cc_start: 0.8629 (tt0) cc_final: 0.8392 (tt0) REVERT: F 250 MET cc_start: 0.9122 (ttp) cc_final: 0.8481 (ttp) REVERT: F 252 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8511 (mmtm) REVERT: G 1 MET cc_start: 0.8636 (ttm) cc_final: 0.8406 (ttp) REVERT: G 89 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8260 (tt0) REVERT: G 93 GLU cc_start: 0.8626 (tt0) cc_final: 0.8387 (tt0) REVERT: H 250 MET cc_start: 0.9133 (ttp) cc_final: 0.8504 (ttp) REVERT: H 252 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8506 (mmtm) REVERT: H 356 LYS cc_start: 0.8838 (ttpm) cc_final: 0.8463 (tttt) REVERT: I 1 MET cc_start: 0.8661 (ttm) cc_final: 0.8430 (ttp) REVERT: I 89 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8240 (tt0) REVERT: J 250 MET cc_start: 0.9130 (ttp) cc_final: 0.8500 (ttp) REVERT: J 252 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8523 (mmtm) REVERT: K 1 MET cc_start: 0.8655 (ttm) cc_final: 0.8430 (ttp) REVERT: K 89 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8247 (tt0) REVERT: L 250 MET cc_start: 0.9132 (ttp) cc_final: 0.8503 (ttp) REVERT: L 252 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8489 (mmtm) REVERT: L 356 LYS cc_start: 0.8834 (ttpm) cc_final: 0.8450 (tttp) REVERT: M 1 MET cc_start: 0.8632 (ttm) cc_final: 0.8396 (ttp) REVERT: M 89 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8261 (tt0) REVERT: N 250 MET cc_start: 0.9128 (ttp) cc_final: 0.8502 (ttp) REVERT: N 252 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8509 (mmtm) REVERT: N 356 LYS cc_start: 0.8833 (ttpm) cc_final: 0.8467 (tttt) REVERT: O 1 MET cc_start: 0.8634 (ttm) cc_final: 0.8404 (ttp) REVERT: O 89 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8249 (tt0) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.9153 time to fit residues: 558.0127 Evaluate side-chains 475 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 162 optimal weight: 30.0000 chunk 398 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 407 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 278 optimal weight: 0.0270 chunk 280 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN S 36 ASN S 55 HIS B 96 GLN C 55 HIS D 96 GLN D 123 ASN E 55 HIS F 96 GLN G 55 HIS H 96 GLN I 55 HIS J 96 GLN K 55 HIS L 96 GLN L 123 ASN M 55 HIS N 96 GLN N 123 ASN O 55 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.163972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.129134 restraints weight = 135631.970| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.46 r_work: 0.3021 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.2818 rms_B_bonded: 3.46 restraints_weight: 0.1250 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36884 Z= 0.214 Angle : 0.711 8.210 50304 Z= 0.376 Chirality : 0.046 0.170 5384 Planarity : 0.006 0.047 6520 Dihedral : 5.424 22.842 5136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.60 % Allowed : 5.15 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 4560 helix: 1.83 (0.12), residues: 1784 sheet: -0.96 (0.17), residues: 712 loop : 0.04 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 253 TYR 0.025 0.003 TYR I 61 PHE 0.030 0.003 PHE A 345 TRP 0.021 0.002 TRP L 70 HIS 0.013 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (36880) covalent geometry : angle 0.70957 / 0.38 (50296) SS BOND : bond 0.01404 / 0.70 ( 4) SS BOND : angle 3.67985 / 2.31 ( 8) hydrogen bonds : bond 0.05260 / 3.43 ( 1664) hydrogen bonds : angle 6.80314 / 4.93 ( 4592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 496 time to evaluate : 1.408 Fit side-chains REVERT: A 175 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7436 (ttpt) REVERT: A 252 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8544 (mmtm) REVERT: A 356 LYS cc_start: 0.8732 (ttpm) cc_final: 0.8318 (tttt) REVERT: S 89 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8159 (tt0) REVERT: B 252 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8536 (mmtm) REVERT: B 356 LYS cc_start: 0.8737 (ttpm) cc_final: 0.8315 (tttt) REVERT: C 89 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8151 (tt0) REVERT: C 93 GLU cc_start: 0.8552 (tt0) cc_final: 0.8295 (tt0) REVERT: D 175 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7444 (ttpt) REVERT: D 252 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8523 (mmtm) REVERT: D 356 LYS cc_start: 0.8724 (ttpm) cc_final: 0.8305 (tttt) REVERT: E 89 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8172 (tt0) REVERT: E 93 GLU cc_start: 0.8533 (tt0) cc_final: 0.8279 (tt0) REVERT: F 175 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7414 (ttpt) REVERT: F 252 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8535 (mmtm) REVERT: G 89 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8187 (tt0) REVERT: G 93 GLU cc_start: 0.8544 (tt0) cc_final: 0.8293 (tt0) REVERT: H 252 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8533 (mmtm) REVERT: H 356 LYS cc_start: 0.8738 (ttpm) cc_final: 0.8318 (tttt) REVERT: I 89 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8148 (tt0) REVERT: J 252 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8548 (mmtm) REVERT: J 356 LYS cc_start: 0.8701 (ttpm) cc_final: 0.8308 (tttt) REVERT: K 89 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8158 (tt0) REVERT: L 175 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7444 (ttpt) REVERT: L 252 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8521 (mmtm) REVERT: L 356 LYS cc_start: 0.8701 (ttpm) cc_final: 0.8282 (tttt) REVERT: M 89 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8171 (tt0) REVERT: N 175 LYS cc_start: 0.7641 (ttmm) cc_final: 0.7406 (ttpt) REVERT: N 252 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8540 (mmtm) REVERT: N 356 LYS cc_start: 0.8748 (ttpm) cc_final: 0.8347 (tttt) REVERT: O 89 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8171 (tt0) outliers start: 7 outliers final: 0 residues processed: 496 average time/residue: 0.9242 time to fit residues: 536.1506 Evaluate side-chains 494 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 381 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 297 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 overall best weight: 4.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN S 36 ASN S 48 HIS B 96 GLN C 48 HIS D 96 GLN E 48 HIS F 96 GLN F 123 ASN G 48 HIS H 96 GLN I 36 ASN I 48 HIS J 96 GLN K 48 HIS L 96 GLN M 36 ASN M 48 HIS N 96 GLN O 48 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.164223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.131250 restraints weight = 142375.626| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.05 r_work: 0.3078 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.2847 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 36884 Z= 0.275 Angle : 0.797 9.165 50304 Z= 0.422 Chirality : 0.049 0.174 5384 Planarity : 0.006 0.061 6520 Dihedral : 5.548 23.582 5136 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.60 % Allowed : 5.49 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4560 helix: 1.62 (0.12), residues: 1784 sheet: -1.13 (0.17), residues: 720 loop : 0.05 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 53 TYR 0.032 0.004 TYR M 61 PHE 0.028 0.004 PHE D 345 TRP 0.021 0.002 TRP L 70 HIS 0.015 0.003 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.27 (36880) covalent geometry : angle 0.79510 / 0.42 (50296) SS BOND : bond 0.01651 / 0.83 ( 4) SS BOND : angle 3.99104 / 2.51 ( 8) hydrogen bonds : bond 0.05749 / 3.76 ( 1664) hydrogen bonds : angle 6.97954 / 5.05 ( 4592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 492 time to evaluate : 1.490 Fit side-chains REVERT: A 252 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8554 (mmtm) REVERT: A 356 LYS cc_start: 0.8714 (ttpm) cc_final: 0.8292 (tttt) REVERT: S 89 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8243 (tt0) REVERT: B 252 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8537 (mmtm) REVERT: B 356 LYS cc_start: 0.8716 (ttpm) cc_final: 0.8306 (tttt) REVERT: C 89 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8236 (tt0) REVERT: D 252 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8518 (mmtm) REVERT: D 356 LYS cc_start: 0.8707 (ttpm) cc_final: 0.8286 (tttt) REVERT: E 89 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8237 (tt0) REVERT: F 252 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8538 (mmtm) REVERT: G 89 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8265 (tt0) REVERT: H 252 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8531 (mmtm) REVERT: H 356 LYS cc_start: 0.8666 (ttpm) cc_final: 0.8240 (tttt) REVERT: I 89 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8239 (tt0) REVERT: J 252 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8545 (mmtm) REVERT: J 356 LYS cc_start: 0.8686 (ttpm) cc_final: 0.8277 (tttt) REVERT: K 89 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8240 (tt0) REVERT: L 252 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8518 (mmtm) REVERT: L 356 LYS cc_start: 0.8747 (ttpm) cc_final: 0.8329 (tttt) REVERT: M 89 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8271 (tt0) REVERT: N 252 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8537 (mmtm) REVERT: N 356 LYS cc_start: 0.8765 (ttpm) cc_final: 0.8362 (tttt) REVERT: O 89 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8236 (tt0) outliers start: 7 outliers final: 0 residues processed: 499 average time/residue: 1.0075 time to fit residues: 584.5816 Evaluate side-chains 490 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 356 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 383 optimal weight: 0.9990 chunk 198 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 96 GLN C 36 ASN D 96 GLN F 96 GLN I 36 ASN K 36 ASN L 96 GLN N 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.169468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.135796 restraints weight = 145349.941| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.42 r_work: 0.3090 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work: 0.2890 rms_B_bonded: 4.06 restraints_weight: 0.1250 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36884 Z= 0.130 Angle : 0.568 5.206 50304 Z= 0.302 Chirality : 0.043 0.163 5384 Planarity : 0.004 0.042 6520 Dihedral : 5.031 21.798 5136 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.66 % Allowed : 5.91 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4560 helix: 1.86 (0.12), residues: 1840 sheet: -0.97 (0.18), residues: 712 loop : 0.15 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 295 TYR 0.013 0.002 TYR F 24 PHE 0.032 0.002 PHE B 345 TRP 0.016 0.001 TRP J 70 HIS 0.006 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (36880) covalent geometry : angle 0.56719 / 0.30 (50296) SS BOND : bond 0.01139 / 0.57 ( 4) SS BOND : angle 2.68130 / 1.68 ( 8) hydrogen bonds : bond 0.04143 / 2.71 ( 1664) hydrogen bonds : angle 6.44618 / 4.69 ( 4592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 1.407 Fit side-chains REVERT: A 252 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8532 (mmtm) REVERT: A 356 LYS cc_start: 0.8799 (ttpm) cc_final: 0.8392 (tttt) REVERT: S 89 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8295 (tt0) REVERT: B 252 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8521 (mmtm) REVERT: B 356 LYS cc_start: 0.8803 (ttpm) cc_final: 0.8393 (tttt) REVERT: C 89 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8327 (tt0) REVERT: D 252 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8510 (mmtm) REVERT: D 356 LYS cc_start: 0.8776 (ttpm) cc_final: 0.8348 (tttt) REVERT: E 89 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8328 (tt0) REVERT: F 252 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8527 (mmtm) REVERT: G 89 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8335 (tt0) REVERT: H 252 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8527 (mmtm) REVERT: H 356 LYS cc_start: 0.8792 (ttpm) cc_final: 0.8377 (tttt) REVERT: I 89 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8325 (tt0) REVERT: J 252 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8538 (mmtm) REVERT: J 356 LYS cc_start: 0.8770 (ttpm) cc_final: 0.8370 (tttt) REVERT: K 89 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8318 (tt0) REVERT: L 252 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8518 (mmtm) REVERT: L 356 LYS cc_start: 0.8765 (ttpm) cc_final: 0.8341 (tttt) REVERT: M 89 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8307 (tt0) REVERT: N 252 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8537 (mmtm) REVERT: N 356 LYS cc_start: 0.8785 (ttpm) cc_final: 0.8372 (tttt) REVERT: O 89 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8328 (tt0) outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.9777 time to fit residues: 576.7221 Evaluate side-chains 488 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 15 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 373 optimal weight: 0.0020 chunk 282 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN S 36 ASN B 96 GLN D 96 GLN F 96 GLN G 36 ASN H 96 GLN I 82 GLN J 96 GLN K 36 ASN K 82 GLN L 96 GLN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.167910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.134187 restraints weight = 138199.643| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.31 r_work: 0.3077 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.2859 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36884 Z= 0.150 Angle : 0.602 5.778 50304 Z= 0.319 Chirality : 0.044 0.166 5384 Planarity : 0.005 0.042 6520 Dihedral : 5.036 22.316 5136 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.84 % Allowed : 5.93 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4560 helix: 1.86 (0.12), residues: 1840 sheet: -0.82 (0.18), residues: 768 loop : 0.28 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 108 TYR 0.017 0.002 TYR E 61 PHE 0.030 0.002 PHE B 345 TRP 0.016 0.001 TRP J 70 HIS 0.009 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (36880) covalent geometry : angle 0.60123 / 0.32 (50296) SS BOND : bond 0.01248 / 0.63 ( 4) SS BOND : angle 2.75301 / 1.73 ( 8) hydrogen bonds : bond 0.04379 / 2.86 ( 1664) hydrogen bonds : angle 6.45960 / 4.70 ( 4592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 505 time to evaluate : 1.402 Fit side-chains REVERT: A 252 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8552 (mmtm) REVERT: A 356 LYS cc_start: 0.8829 (ttpm) cc_final: 0.8412 (tttt) REVERT: S 89 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8341 (tt0) REVERT: B 252 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8542 (mmtm) REVERT: B 356 LYS cc_start: 0.8849 (ttpm) cc_final: 0.8432 (tttt) REVERT: C 89 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8348 (tt0) REVERT: D 252 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8533 (mmtm) REVERT: D 356 LYS cc_start: 0.8813 (ttpm) cc_final: 0.8387 (tttt) REVERT: E 89 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8364 (tt0) REVERT: F 252 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8539 (mmtm) REVERT: F 340 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7973 (mm-30) REVERT: F 356 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8425 (tttt) REVERT: G 89 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8361 (tt0) REVERT: H 252 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8540 (mmtm) REVERT: H 356 LYS cc_start: 0.8835 (ttpm) cc_final: 0.8415 (tttt) REVERT: I 89 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8331 (tt0) REVERT: J 252 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8551 (mmtm) REVERT: J 340 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7989 (mm-30) REVERT: J 356 LYS cc_start: 0.8804 (ttpm) cc_final: 0.8402 (tttt) REVERT: K 89 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8353 (tt0) REVERT: L 252 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8528 (mmtm) REVERT: L 340 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7900 (mm-30) REVERT: L 356 LYS cc_start: 0.8807 (ttpm) cc_final: 0.8372 (tttt) REVERT: M 89 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8357 (tt0) REVERT: N 252 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8544 (mmtm) REVERT: N 356 LYS cc_start: 0.8826 (ttpm) cc_final: 0.8408 (tttt) REVERT: O 89 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8354 (tt0) outliers start: 8 outliers final: 0 residues processed: 505 average time/residue: 0.9283 time to fit residues: 548.5815 Evaluate side-chains 494 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 210 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 416 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 288 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN S 36 ASN B 96 GLN C 36 ASN D 96 GLN E 36 ASN F 96 GLN G 36 ASN H 96 GLN I 36 ASN I 82 GLN J 96 GLN K 36 ASN L 96 GLN M 36 ASN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130800 restraints weight = 135461.233| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.49 r_work: 0.3033 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work: 0.2814 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36884 Z= 0.212 Angle : 0.695 8.182 50304 Z= 0.367 Chirality : 0.046 0.175 5384 Planarity : 0.005 0.046 6520 Dihedral : 5.266 23.207 5136 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.02 % Allowed : 6.07 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 4560 helix: 1.89 (0.12), residues: 1784 sheet: -1.02 (0.17), residues: 824 loop : 0.30 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 258 TYR 0.026 0.003 TYR C 61 PHE 0.028 0.003 PHE D 345 TRP 0.017 0.002 TRP N 70 HIS 0.015 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (36880) covalent geometry : angle 0.69344 / 0.37 (50296) SS BOND : bond 0.01472 / 0.74 ( 4) SS BOND : angle 3.14974 / 1.98 ( 8) hydrogen bonds : bond 0.05050 / 3.30 ( 1664) hydrogen bonds : angle 6.72464 / 4.88 ( 4592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 499 time to evaluate : 1.426 Fit side-chains REVERT: A 252 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8567 (mmtm) REVERT: A 356 LYS cc_start: 0.8788 (ttpm) cc_final: 0.8357 (tttt) REVERT: S 89 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8262 (tt0) REVERT: B 252 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8550 (mmtm) REVERT: B 356 LYS cc_start: 0.8805 (ttpm) cc_final: 0.8374 (tttt) REVERT: C 89 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8307 (tt0) REVERT: D 252 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8533 (mmtm) REVERT: D 356 LYS cc_start: 0.8774 (ttpm) cc_final: 0.8326 (tttt) REVERT: E 89 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8305 (tt0) REVERT: F 252 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8551 (mmtm) REVERT: F 356 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8362 (tttt) REVERT: G 89 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8309 (tt0) REVERT: H 252 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8552 (mmtm) REVERT: H 356 LYS cc_start: 0.8789 (ttpm) cc_final: 0.8352 (tttt) REVERT: I 89 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8266 (tt0) REVERT: J 252 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8564 (mmtm) REVERT: J 356 LYS cc_start: 0.8768 (ttpm) cc_final: 0.8357 (tttt) REVERT: K 89 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8282 (tt0) REVERT: L 252 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8539 (mmtm) REVERT: L 340 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7888 (mm-30) REVERT: L 356 LYS cc_start: 0.8763 (ttpm) cc_final: 0.8322 (tttt) REVERT: M 89 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8279 (tt0) REVERT: N 252 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8554 (mmtm) REVERT: N 340 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7900 (mm-30) REVERT: N 356 LYS cc_start: 0.8780 (ttpm) cc_final: 0.8361 (tttt) REVERT: O 89 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8270 (tt0) outliers start: 15 outliers final: 0 residues processed: 506 average time/residue: 0.9646 time to fit residues: 571.8415 Evaluate side-chains 490 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 156 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 374 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 315 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 410 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 36 ASN B 96 GLN C 36 ASN D 96 GLN E 36 ASN F 96 GLN G 36 ASN I 36 ASN I 82 GLN K 36 ASN L 96 GLN M 36 ASN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.165545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.130891 restraints weight = 141626.289| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.55 r_work: 0.3036 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.2818 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36884 Z= 0.202 Angle : 0.683 7.744 50304 Z= 0.361 Chirality : 0.046 0.172 5384 Planarity : 0.005 0.041 6520 Dihedral : 5.254 23.020 5136 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.68 % Allowed : 6.54 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.12), residues: 4560 helix: 1.87 (0.12), residues: 1784 sheet: -0.96 (0.17), residues: 816 loop : 0.34 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 253 TYR 0.023 0.003 TYR O 61 PHE 0.028 0.003 PHE A 345 TRP 0.017 0.002 TRP J 70 HIS 0.015 0.002 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (36880) covalent geometry : angle 0.68157 / 0.36 (50296) SS BOND : bond 0.01428 / 0.72 ( 4) SS BOND : angle 3.14154 / 1.97 ( 8) hydrogen bonds : bond 0.04968 / 3.25 ( 1664) hydrogen bonds : angle 6.72666 / 4.88 ( 4592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 492 time to evaluate : 1.173 Fit side-chains REVERT: A 252 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8553 (mmtm) REVERT: A 356 LYS cc_start: 0.8762 (ttpm) cc_final: 0.8341 (tttt) REVERT: S 89 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8227 (tt0) REVERT: B 252 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8544 (mmtm) REVERT: B 356 LYS cc_start: 0.8747 (ttpm) cc_final: 0.8316 (tttt) REVERT: C 89 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8278 (tt0) REVERT: D 252 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8532 (mmtm) REVERT: D 356 LYS cc_start: 0.8726 (ttpm) cc_final: 0.8285 (tttt) REVERT: E 89 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8286 (tt0) REVERT: F 252 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8545 (mmtm) REVERT: F 356 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8317 (tttt) REVERT: G 89 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8294 (tt0) REVERT: H 252 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8546 (mmtm) REVERT: H 356 LYS cc_start: 0.8751 (ttpm) cc_final: 0.8320 (tttt) REVERT: I 89 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8249 (tt0) REVERT: J 252 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8556 (mmtm) REVERT: J 356 LYS cc_start: 0.8706 (ttpm) cc_final: 0.8297 (tttt) REVERT: K 89 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8261 (tt0) REVERT: L 252 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8535 (mmtm) REVERT: L 340 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7862 (mm-30) REVERT: L 356 LYS cc_start: 0.8729 (ttpm) cc_final: 0.8293 (tttt) REVERT: M 89 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8233 (tt0) REVERT: N 252 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8551 (mmtm) REVERT: N 356 LYS cc_start: 0.8740 (ttpm) cc_final: 0.8323 (tttt) REVERT: O 89 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8243 (tt0) outliers start: 2 outliers final: 1 residues processed: 493 average time/residue: 0.9083 time to fit residues: 524.1959 Evaluate side-chains 486 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 366 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 369 optimal weight: 0.8980 chunk 417 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 283 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 36 ASN B 96 GLN C 36 ASN D 96 GLN E 36 ASN F 96 GLN G 36 ASN H 96 GLN I 36 ASN I 82 GLN K 36 ASN L 96 GLN M 36 ASN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.167106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.132461 restraints weight = 142345.640| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.56 r_work: 0.3052 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2873 rms_B_bonded: 3.29 restraints_weight: 0.1250 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36884 Z= 0.164 Angle : 0.622 6.120 50304 Z= 0.330 Chirality : 0.044 0.168 5384 Planarity : 0.005 0.041 6520 Dihedral : 5.118 22.544 5136 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.63 % Allowed : 6.75 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4560 helix: 1.95 (0.12), residues: 1792 sheet: -0.84 (0.18), residues: 768 loop : 0.30 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 108 TYR 0.017 0.002 TYR K 61 PHE 0.029 0.002 PHE D 345 TRP 0.016 0.001 TRP H 70 HIS 0.011 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (36880) covalent geometry : angle 0.62123 / 0.33 (50296) SS BOND : bond 0.01307 / 0.65 ( 4) SS BOND : angle 2.91143 / 1.83 ( 8) hydrogen bonds : bond 0.04541 / 2.97 ( 1664) hydrogen bonds : angle 6.56666 / 4.77 ( 4592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.360 Fit side-chains REVERT: A 252 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8531 (mmtm) REVERT: A 356 LYS cc_start: 0.8669 (ttpm) cc_final: 0.8267 (tttt) REVERT: S 89 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8152 (tt0) REVERT: B 252 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8527 (mmtm) REVERT: B 356 LYS cc_start: 0.8731 (ttpm) cc_final: 0.8310 (tttt) REVERT: C 89 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8182 (tt0) REVERT: D 252 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8511 (mmtm) REVERT: D 340 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7884 (mm-30) REVERT: D 356 LYS cc_start: 0.8676 (ttpm) cc_final: 0.8249 (tttt) REVERT: E 89 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8182 (tt0) REVERT: F 252 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8526 (mmtm) REVERT: F 340 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7798 (mm-30) REVERT: F 356 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8231 (tttt) REVERT: G 89 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8191 (tt0) REVERT: H 252 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8533 (mmtm) REVERT: H 356 LYS cc_start: 0.8694 (ttpm) cc_final: 0.8283 (tttt) REVERT: I 89 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8160 (tt0) REVERT: J 252 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8542 (mmtm) REVERT: J 340 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7863 (mm-30) REVERT: J 356 LYS cc_start: 0.8663 (ttpm) cc_final: 0.8276 (tttt) REVERT: K 89 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8181 (tt0) REVERT: L 252 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8524 (mmtm) REVERT: L 340 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7797 (mm-30) REVERT: L 356 LYS cc_start: 0.8681 (ttpm) cc_final: 0.8257 (tttt) REVERT: M 89 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8162 (tt0) REVERT: N 252 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8537 (mmtm) REVERT: N 340 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7779 (mm-30) REVERT: N 356 LYS cc_start: 0.8649 (ttpm) cc_final: 0.8255 (tttt) REVERT: O 89 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8152 (tt0) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.9063 time to fit residues: 517.1080 Evaluate side-chains 488 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 368 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 365 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 334 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 36 ASN B 96 GLN C 36 ASN D 96 GLN E 36 ASN F 96 GLN G 36 ASN H 96 GLN I 36 ASN I 82 GLN K 36 ASN L 96 GLN M 36 ASN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.164174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.129547 restraints weight = 141646.773| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.53 r_work: 0.3007 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.2793 rms_B_bonded: 4.00 restraints_weight: 0.1250 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 36884 Z= 0.261 Angle : 0.764 8.947 50304 Z= 0.406 Chirality : 0.048 0.179 5384 Planarity : 0.006 0.058 6520 Dihedral : 5.393 23.587 5136 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.63 % Allowed : 6.93 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4560 helix: 1.73 (0.12), residues: 1784 sheet: -1.04 (0.17), residues: 824 loop : 0.23 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 53 TYR 0.032 0.003 TYR M 61 PHE 0.027 0.003 PHE J 311 TRP 0.016 0.002 TRP J 70 HIS 0.016 0.002 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (36880) covalent geometry : angle 0.76298 / 0.41 (50296) SS BOND : bond 0.01636 / 0.82 ( 4) SS BOND : angle 3.43340 / 2.16 ( 8) hydrogen bonds : bond 0.05482 / 3.59 ( 1664) hydrogen bonds : angle 6.90477 / 5.00 ( 4592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.419 Fit side-chains REVERT: A 252 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8567 (mmtm) REVERT: A 356 LYS cc_start: 0.8807 (ttpm) cc_final: 0.8366 (tttt) REVERT: S 89 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8272 (tt0) REVERT: B 252 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8559 (mmtm) REVERT: B 356 LYS cc_start: 0.8821 (ttpm) cc_final: 0.8368 (tttt) REVERT: C 89 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8278 (tt0) REVERT: D 252 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8541 (mmtm) REVERT: D 356 LYS cc_start: 0.8790 (ttpm) cc_final: 0.8343 (tttt) REVERT: E 89 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8280 (tt0) REVERT: F 252 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8554 (mmtm) REVERT: F 356 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8343 (tttt) REVERT: G 89 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8293 (tt0) REVERT: H 252 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8558 (mmtm) REVERT: H 356 LYS cc_start: 0.8787 (ttpm) cc_final: 0.8350 (tttt) REVERT: I 89 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8269 (tt0) REVERT: J 252 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8567 (mmtm) REVERT: J 356 LYS cc_start: 0.8763 (ttpm) cc_final: 0.8347 (tttt) REVERT: K 89 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8266 (tt0) REVERT: L 252 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8548 (mmtm) REVERT: L 340 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7917 (mm-30) REVERT: L 356 LYS cc_start: 0.8773 (ttpm) cc_final: 0.8328 (tttt) REVERT: M 89 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8283 (tt0) REVERT: N 252 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8557 (mmtm) REVERT: N 340 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7871 (mm-30) REVERT: N 356 LYS cc_start: 0.8783 (ttpm) cc_final: 0.8349 (tttt) REVERT: O 89 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8253 (tt0) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.9298 time to fit residues: 544.1050 Evaluate side-chains 496 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 312 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 36 ASN B 96 GLN C 36 ASN D 96 GLN E 36 ASN F 96 GLN G 36 ASN I 36 ASN I 82 GLN K 36 ASN L 96 GLN M 36 ASN N 96 GLN O 36 ASN O 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.164548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.130086 restraints weight = 138508.317| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.51 r_work: 0.3046 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.2851 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36884 Z= 0.244 Angle : 0.742 8.541 50304 Z= 0.394 Chirality : 0.048 0.177 5384 Planarity : 0.006 0.049 6520 Dihedral : 5.381 23.191 5136 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.63 % Allowed : 6.96 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4560 helix: 1.64 (0.12), residues: 1784 sheet: -1.02 (0.17), residues: 824 loop : 0.20 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 258 TYR 0.027 0.003 TYR O 61 PHE 0.027 0.003 PHE A 345 TRP 0.016 0.002 TRP H 70 HIS 0.016 0.002 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (36880) covalent geometry : angle 0.74120 / 0.39 (50296) SS BOND : bond 0.01535 / 0.77 ( 4) SS BOND : angle 3.33664 / 2.10 ( 8) hydrogen bonds : bond 0.05352 / 3.51 ( 1664) hydrogen bonds : angle 6.89117 / 4.99 ( 4592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23352.67 seconds wall clock time: 397 minutes 10.25 seconds (23830.25 seconds total)