Starting phenix.real_space_refine on Sun Aug 9 21:11:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l58_62824/08_2026/9l58_62824.map" } resolution = 1.76 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= 0.016 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 208 5.16 5 C 23304 2.51 5 N 6136 2.21 5 O 8584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 176 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: 38232 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3487 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3400 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 413} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 435, 3400 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 413} Chain breaks: 2 bond proxies already assigned to first conformer: 3378 Chain: "S" Number of atoms: 1045 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 992 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 119, 989 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 1 bond proxies already assigned to first conformer: 961 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'SO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "S" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "H" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "L" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "N" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} 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: 96 residue: pdb=" N AVAL A 57 " occ=0.58 ... (12 atoms not shown) pdb=" CG2BVAL A 57 " occ=0.42 residue: pdb=" N AASN A 207 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 207 " occ=0.50 residue: pdb=" N ASER A 379 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A 379 " occ=0.49 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: pdb=" N ALEU S 74 " occ=0.67 ... (14 atoms not shown) pdb=" CD2BLEU S 74 " occ=0.33 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 AVAL B 57 " occ=0.58 ... (12 atoms not shown) pdb=" CG2BVAL B 57 " occ=0.42 residue: pdb=" N AASN B 207 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 207 " occ=0.50 ... (remaining 84 not shown) Time building chain proxies: 6.75, per 1000 atoms: 0.18 Number of scatterers: 38232 At special positions: 0 Unit cell: (141.81, 141.81, 122.67, 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 208 16.00 O 8584 8.00 N 6136 7.00 C 23304 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=2.06 Simple disulfide: pdb=" SG ACYS B 247 " - pdb=" SG ACYS J 247 " distance=2.06 Simple disulfide: pdb=" SG ACYS D 247 " - pdb=" SG ACYS N 247 " distance=2.06 Simple disulfide: pdb=" SG ACYS F 247 " - pdb=" SG ACYS L 247 " distance=2.06 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: 3.43 Conformation dependent library (CDL) restraints added in 2.6 seconds 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8480 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 32 sheets defined 48.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER A 61 " --> pdb=" O BVAL A 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL S 83 " --> pdb=" O ASP S 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER B 61 " --> pdb=" O BVAL B 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER D 61 " --> pdb=" O BVAL D 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER F 61 " --> pdb=" O BVAL F 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU F 460 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER H 61 " --> pdb=" O BVAL H 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 450 " --> pdb=" O ARG H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU H 460 " --> pdb=" O ALA H 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL I 83 " --> pdb=" O ASP I 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER J 61 " --> pdb=" O BVAL J 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 75 Processing helix chain 'J' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR J 80 " --> pdb=" O SER J 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE J 301 " --> pdb=" O MET J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'J' and resid 412 through 433 Processing helix chain 'J' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN J 442 " --> pdb=" O ALA J 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU J 443 " --> pdb=" O VAL J 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS J 450 " --> pdb=" O ARG J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU J 460 " --> pdb=" O ALA J 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER L 61 " --> pdb=" O BVAL L 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER L 62 " --> pdb=" O ALA L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 75 Processing helix chain 'L' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE L 301 " --> pdb=" O MET L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN L 442 " --> pdb=" O ALA L 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU L 443 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS L 450 " --> pdb=" O ARG L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU L 460 " --> pdb=" O ALA L 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A pdb=" N VAL M 83 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 62 removed outlier: 4.485A pdb=" N SER N 61 " --> pdb=" O BVAL N 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 75 Processing helix chain 'N' and resid 76 through 81 removed outlier: 3.626A pdb=" N TYR N 80 " --> pdb=" O SER N 76 " (cutoff:3.500A) 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: 3.561A 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: 3.866A pdb=" N ILE N 301 " --> pdb=" O MET N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 322 removed outlier: 3.667A 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 403 through 408 Processing helix chain 'N' and resid 412 through 433 Processing helix chain 'N' and resid 436 through 450 removed outlier: 6.446A pdb=" N ASN N 442 " --> pdb=" O ALA N 438 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU N 443 " --> pdb=" O VAL N 439 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS N 450 " --> pdb=" O ARG N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 462 removed outlier: 3.530A pdb=" N GLU N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.112A 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 89 removed outlier: 5.629A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS A 294 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER A 379 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY A 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL S 42 " --> pdb=" O TRP S 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 172 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER B 379 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL C 42 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU D 170 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS D 201 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS D 172 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER D 379 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN D 401 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 378 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY D 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL E 42 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS F 294 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER F 379 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY F 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL G 42 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS H 172 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS H 294 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER H 379 " --> pdb=" O ILE H 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY H 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL I 42 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS J 86 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU J 37 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU J 138 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU J 170 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS J 201 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS J 172 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS J 294 " --> pdb=" O VAL J 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE J 326 " --> pdb=" O VAL J 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER J 379 " --> pdb=" O ILE J 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE J 402 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY J 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL K 42 " --> pdb=" O TRP K 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS L 84 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA L 102 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS L 86 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU L 37 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU L 138 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU L 170 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS L 201 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS L 172 " --> pdb=" O LYS L 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR L 200 " --> pdb=" O TYR L 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN L 241 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS L 238 " --> pdb=" O ILE L 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET L 266 " --> pdb=" O HIS L 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU L 240 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP L 268 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL L 265 " --> pdb=" O HIS L 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS L 294 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS L 267 " --> pdb=" O HIS L 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE L 326 " --> pdb=" O VAL L 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER L 379 " --> pdb=" O ILE L 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN L 401 " --> pdb=" O PRO L 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA L 378 " --> pdb=" O GLN L 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU L 169 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE L 402 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY L 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL M 42 " --> pdb=" O TRP M 70 " (cutoff:3.500A) removed outlier: 6.481A 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 89 removed outlier: 5.629A pdb=" N CYS N 84 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA N 102 " --> pdb=" O CYS N 84 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS N 86 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU N 37 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU N 138 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 6.599A 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 173 removed outlier: 6.387A pdb=" N LEU N 170 " --> pdb=" O PHE N 199 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS N 201 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS N 172 " --> pdb=" O LYS N 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR N 200 " --> pdb=" O TYR N 239 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN N 241 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N HIS N 238 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET N 266 " --> pdb=" O HIS N 238 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU N 240 " --> pdb=" O MET N 266 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP N 268 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL N 265 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS N 294 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N HIS N 267 " --> pdb=" O HIS N 294 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE N 326 " --> pdb=" O VAL N 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASER N 379 " --> pdb=" O ILE N 326 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN N 401 " --> pdb=" O PRO N 376 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA N 378 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU N 169 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE N 402 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY N 171 " --> pdb=" O PHE 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: 4.552A pdb=" N VAL O 42 " --> pdb=" O TRP O 70 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE O 99 " --> pdb=" O ALA O 117 " (cutoff:3.500A) 1672 hydrogen bonds defined for protein. 4552 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: 9.41 Time building geometry restraints manager: 4.71 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: 8600 1.33 - 1.45: 10376 1.45 - 1.57: 18216 1.57 - 1.69: 8 1.69 - 1.81: 272 Bond restraints: 37472 Sorted by residual: bond pdb=" CG GLU L 60 " pdb=" CD GLU L 60 " ideal model delta sigma weight residual 1.516 1.702 -0.186 2.50e-02 1.60e+03 5.56e+01 bond pdb=" CG GLU N 60 " pdb=" CD GLU N 60 " ideal model delta sigma weight residual 1.516 1.702 -0.186 2.50e-02 1.60e+03 5.56e+01 bond pdb=" CG GLU D 60 " pdb=" CD GLU D 60 " ideal model delta sigma weight residual 1.516 1.702 -0.186 2.50e-02 1.60e+03 5.56e+01 bond pdb=" CG GLU F 60 " pdb=" CD GLU F 60 " ideal model delta sigma weight residual 1.516 1.702 -0.186 2.50e-02 1.60e+03 5.56e+01 bond pdb=" CG GLU H 60 " pdb=" CD GLU H 60 " ideal model delta sigma weight residual 1.516 1.702 -0.186 2.50e-02 1.60e+03 5.56e+01 ... (remaining 37467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 39600 1.62 - 3.25: 9120 3.25 - 4.87: 1920 4.87 - 6.50: 440 6.50 - 8.12: 120 Bond angle restraints: 51200 Sorted by residual: angle pdb=" CA PHE K 50 " pdb=" CB PHE K 50 " pdb=" CG PHE K 50 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA PHE O 50 " pdb=" CB PHE O 50 " pdb=" CG PHE O 50 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA PHE G 50 " pdb=" CB PHE G 50 " pdb=" CG PHE G 50 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA PHE E 50 " pdb=" CB PHE E 50 " pdb=" CG PHE E 50 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA PHE S 50 " pdb=" CB PHE S 50 " pdb=" CG PHE S 50 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.22e+01 ... (remaining 51195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 20560 17.08 - 34.17: 1272 34.17 - 51.25: 264 51.25 - 68.34: 148 68.34 - 85.42: 32 Dihedral angle restraints: 22276 sinusoidal: 8820 harmonic: 13456 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 -26.48 -59.52 1 1.00e+01 1.00e-02 4.73e+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 -26.48 -59.52 1 1.00e+01 1.00e-02 4.73e+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 -26.48 -59.52 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 22273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2904 0.055 - 0.110: 1680 0.110 - 0.165: 720 0.165 - 0.219: 168 0.219 - 0.274: 32 Chirality restraints: 5504 Sorted by residual: chirality pdb=" CA PHE N 345 " pdb=" N PHE N 345 " pdb=" C PHE N 345 " pdb=" CB PHE N 345 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE J 345 " pdb=" N PHE J 345 " pdb=" C PHE J 345 " pdb=" CB PHE J 345 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE F 345 " pdb=" N PHE F 345 " pdb=" C PHE F 345 " pdb=" CB PHE F 345 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 5501 not shown) Planarity restraints: 6656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 269 " 0.067 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR L 269 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR L 269 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR L 269 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR L 269 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR L 269 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR L 269 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 269 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 269 " -0.067 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR N 269 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR N 269 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR N 269 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR N 269 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR N 269 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR N 269 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR N 269 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 269 " 0.067 2.00e-02 2.50e+03 3.41e-02 2.32e+01 pdb=" CG TYR B 269 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 269 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 269 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 269 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 269 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 269 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 269 " 0.033 2.00e-02 2.50e+03 ... (remaining 6653 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 4 1.85 - 2.61: 1528 2.61 - 3.37: 56264 3.37 - 4.14: 124220 4.14 - 4.90: 211576 Nonbonded interactions: 393592 Sorted by model distance: nonbonded pdb=" O HOH A 749 " pdb=" O HOH H 749 " model vdw 1.083 3.040 nonbonded pdb=" O HOH D 749 " pdb=" O HOH N 749 " model vdw 1.083 3.040 nonbonded pdb=" O HOH F 749 " pdb=" O HOH L 749 " model vdw 1.083 3.040 nonbonded pdb=" O HOH B 749 " pdb=" O HOH J 749 " model vdw 1.083 3.040 nonbonded pdb=" O GLU B 204 " pdb=" O HOH B 601 " model vdw 1.928 3.040 ... (remaining 393587 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=0.26 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 36.690 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.120 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 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 0.186 37476 Z= 0.645 Angle : 1.539 11.518 51208 Z= 1.003 Chirality : 0.078 0.274 5504 Planarity : 0.013 0.186 6656 Dihedral : 13.246 85.423 13784 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.49 % Favored : 96.32 % Rotamer: Outliers : 1.03 % Allowed : 3.09 % Favored : 95.88 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.23 % 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: -0.98 (0.11), residues: 4696 helix: -0.42 (0.10), residues: 1824 sheet: -0.87 (0.16), residues: 776 loop : -0.59 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.004 ARG N 253 TYR 0.067 0.009 TYR L 269 PHE 0.041 0.008 PHE F 402 TRP 0.028 0.007 TRP I 4 HIS 0.021 0.007 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.64 (37472) covalent geometry : angle 1.53234 / 1.00 (51200) SS BOND : bond 0.02871 / 1.44 ( 4) SS BOND : angle 11.51828 / 5.16 ( 8) hydrogen bonds : bond 0.15156 / 10.10 ( 1672) hydrogen bonds : angle 8.03401 / 5.85 ( 4552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 546 time to evaluate : 1.207 Fit side-chains REVERT: A 123 ASN cc_start: 0.5311 (p0) cc_final: 0.5050 (p0) REVERT: A 127 PHE cc_start: 0.4285 (OUTLIER) cc_final: 0.3755 (m-10) REVERT: A 303 ARG cc_start: 0.5956 (tpt-90) cc_final: 0.5650 (tpt-90) REVERT: A 305 LYS cc_start: 0.6567 (mptp) cc_final: 0.5520 (mmpt) REVERT: A 356 LYS cc_start: 0.6748 (ttpt) cc_final: 0.5982 (tttp) REVERT: S 7 ILE cc_start: 0.6692 (pt) cc_final: 0.6376 (pp) REVERT: S 37 LYS cc_start: 0.6390 (mmtt) cc_final: 0.6065 (mmmm) REVERT: S 39 ILE cc_start: 0.7357 (mp) cc_final: 0.7147 (mm) REVERT: S 48 HIS cc_start: 0.6773 (m-70) cc_final: 0.6556 (m90) REVERT: S 85 LYS cc_start: 0.6236 (tttt) cc_final: 0.5963 (ttmt) REVERT: S 86 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6718 (mm-30) REVERT: B 123 ASN cc_start: 0.5306 (p0) cc_final: 0.5066 (p0) REVERT: B 127 PHE cc_start: 0.4291 (OUTLIER) cc_final: 0.3765 (m-10) REVERT: B 204 GLU cc_start: 0.5137 (pm20) cc_final: 0.4824 (pm20) REVERT: B 303 ARG cc_start: 0.5939 (tpt-90) cc_final: 0.5632 (tpt-90) REVERT: B 305 LYS cc_start: 0.6551 (mptp) cc_final: 0.5506 (mmpt) REVERT: B 356 LYS cc_start: 0.6813 (ttpt) cc_final: 0.6044 (tttp) REVERT: C 7 ILE cc_start: 0.6697 (pt) cc_final: 0.6381 (pp) REVERT: C 37 LYS cc_start: 0.6489 (mmtt) cc_final: 0.6204 (mmmm) REVERT: C 39 ILE cc_start: 0.7448 (mp) cc_final: 0.7235 (mm) REVERT: C 48 HIS cc_start: 0.6782 (m-70) cc_final: 0.6565 (m90) REVERT: C 85 LYS cc_start: 0.6335 (tttt) cc_final: 0.6087 (ttmt) REVERT: D 127 PHE cc_start: 0.4300 (OUTLIER) cc_final: 0.3769 (m-10) REVERT: D 303 ARG cc_start: 0.5957 (tpt-90) cc_final: 0.5650 (tpt-90) REVERT: D 305 LYS cc_start: 0.6685 (mptp) cc_final: 0.5618 (mmpt) REVERT: D 356 LYS cc_start: 0.6768 (ttpt) cc_final: 0.5998 (tttp) REVERT: E 7 ILE cc_start: 0.6678 (pt) cc_final: 0.6360 (pp) REVERT: E 37 LYS cc_start: 0.6440 (mmtt) cc_final: 0.6158 (mmmm) REVERT: E 48 HIS cc_start: 0.6780 (m-70) cc_final: 0.6564 (m90) REVERT: E 85 LYS cc_start: 0.6330 (tttt) cc_final: 0.6100 (ttmt) REVERT: F 127 PHE cc_start: 0.4286 (OUTLIER) cc_final: 0.3771 (m-10) REVERT: F 303 ARG cc_start: 0.5972 (tpt-90) cc_final: 0.5663 (tpt-90) REVERT: F 305 LYS cc_start: 0.6680 (mptp) cc_final: 0.5623 (mmpt) REVERT: F 356 LYS cc_start: 0.6762 (ttpt) cc_final: 0.5996 (tttp) REVERT: G 7 ILE cc_start: 0.6685 (pt) cc_final: 0.6354 (pp) REVERT: G 37 LYS cc_start: 0.6402 (mmtt) cc_final: 0.6119 (mmmm) REVERT: G 48 HIS cc_start: 0.6775 (m-70) cc_final: 0.6558 (m90) REVERT: H 123 ASN cc_start: 0.5287 (p0) cc_final: 0.5049 (p0) REVERT: H 127 PHE cc_start: 0.4313 (OUTLIER) cc_final: 0.3785 (m-10) REVERT: H 204 GLU cc_start: 0.5135 (pm20) cc_final: 0.4822 (pm20) REVERT: H 303 ARG cc_start: 0.5949 (tpt-90) cc_final: 0.5644 (tpt-90) REVERT: H 305 LYS cc_start: 0.6564 (mptp) cc_final: 0.5518 (mmpt) REVERT: H 356 LYS cc_start: 0.6786 (ttpt) cc_final: 0.6015 (tttp) REVERT: H 392 GLU cc_start: 0.6049 (tt0) cc_final: 0.5598 (tm-30) REVERT: I 7 ILE cc_start: 0.6699 (pt) cc_final: 0.6380 (pp) REVERT: I 37 LYS cc_start: 0.6500 (mmtt) cc_final: 0.6213 (mmmm) REVERT: I 39 ILE cc_start: 0.7438 (mp) cc_final: 0.7233 (mm) REVERT: I 48 HIS cc_start: 0.6790 (m-70) cc_final: 0.6570 (m90) REVERT: I 85 LYS cc_start: 0.6200 (tttt) cc_final: 0.5968 (ttmt) REVERT: I 86 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6710 (mm-30) REVERT: J 123 ASN cc_start: 0.5303 (p0) cc_final: 0.5044 (p0) REVERT: J 127 PHE cc_start: 0.4288 (OUTLIER) cc_final: 0.3758 (m-10) REVERT: J 303 ARG cc_start: 0.5926 (tpt-90) cc_final: 0.5622 (tpt-90) REVERT: J 305 LYS cc_start: 0.6597 (mptp) cc_final: 0.5556 (mmpt) REVERT: J 356 LYS cc_start: 0.6721 (ttpt) cc_final: 0.5958 (tttp) REVERT: K 7 ILE cc_start: 0.6676 (pt) cc_final: 0.6359 (pp) REVERT: K 37 LYS cc_start: 0.6488 (mmtt) cc_final: 0.6201 (mmmm) REVERT: K 39 ILE cc_start: 0.7403 (mp) cc_final: 0.7184 (mm) REVERT: K 48 HIS cc_start: 0.6788 (m-70) cc_final: 0.6568 (m90) REVERT: K 85 LYS cc_start: 0.6121 (tttt) cc_final: 0.5879 (ttmt) REVERT: K 86 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6634 (mm-30) REVERT: L 123 ASN cc_start: 0.5260 (p0) cc_final: 0.5022 (p0) REVERT: L 127 PHE cc_start: 0.4330 (OUTLIER) cc_final: 0.3793 (m-10) REVERT: L 204 GLU cc_start: 0.5161 (pm20) cc_final: 0.4812 (pm20) REVERT: L 303 ARG cc_start: 0.5924 (tpt-90) cc_final: 0.5620 (tpt-90) REVERT: L 305 LYS cc_start: 0.6652 (mptp) cc_final: 0.5594 (mmpt) REVERT: L 356 LYS cc_start: 0.6780 (ttpt) cc_final: 0.6015 (tttp) REVERT: M 7 ILE cc_start: 0.6692 (pt) cc_final: 0.6374 (pp) REVERT: M 37 LYS cc_start: 0.6520 (mmtt) cc_final: 0.6235 (mmmm) REVERT: M 48 HIS cc_start: 0.6753 (m-70) cc_final: 0.6535 (m90) REVERT: M 86 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6684 (mm-30) REVERT: N 127 PHE cc_start: 0.4342 (OUTLIER) cc_final: 0.3810 (m-10) REVERT: N 303 ARG cc_start: 0.5967 (tpt-90) cc_final: 0.5660 (tpt-90) REVERT: N 305 LYS cc_start: 0.6683 (mptp) cc_final: 0.5623 (mmpt) REVERT: N 356 LYS cc_start: 0.6735 (ttpt) cc_final: 0.5967 (tttp) REVERT: O 7 ILE cc_start: 0.6667 (pt) cc_final: 0.6349 (pp) REVERT: O 37 LYS cc_start: 0.6452 (mmtt) cc_final: 0.6167 (mmmm) REVERT: O 48 HIS cc_start: 0.6756 (m-70) cc_final: 0.6537 (m90) REVERT: O 85 LYS cc_start: 0.6123 (tttt) cc_final: 0.5896 (ttmt) REVERT: O 86 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6625 (mm-30) outliers start: 32 outliers final: 0 residues processed: 570 average time/residue: 0.9662 time to fit residues: 645.5902 Evaluate side-chains 515 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 507 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain N residue 127 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 ASN S 82 GLN B 420 ASN C 82 GLN D 420 ASN E 82 GLN F 420 ASN G 82 GLN H 420 ASN I 82 GLN J 420 ASN L 420 ASN M 82 GLN N 420 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 = 0.3973 r_free = 0.3973 target = 0.181704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.141496 restraints weight = 146639.207| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.78 r_work: 0.3087 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.2917 rms_B_bonded: 3.48 restraints_weight: 0.1250 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37476 Z= 0.167 Angle : 0.665 5.577 51208 Z= 0.356 Chirality : 0.045 0.160 5504 Planarity : 0.005 0.037 6656 Dihedral : 6.042 56.408 5248 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.49 % Allowed : 6.01 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.49 (0.12), residues: 4696 helix: 1.55 (0.12), residues: 1784 sheet: -1.09 (0.16), residues: 688 loop : -0.12 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 350 TYR 0.015 0.002 TYR D 283 PHE 0.037 0.003 PHE D 345 TRP 0.007 0.001 TRP J 368 HIS 0.012 0.001 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (37472) covalent geometry : angle 0.66272 / 0.35 (51200) SS BOND : bond 0.01327 / 0.66 ( 4) SS BOND : angle 4.24499 / 1.90 ( 8) hydrogen bonds : bond 0.04669 / 3.13 ( 1672) hydrogen bonds : angle 6.40330 / 4.70 ( 4552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 552 time to evaluate : 1.211 Fit side-chains REVERT: A 305 LYS cc_start: 0.8331 (mptp) cc_final: 0.7889 (mmpt) REVERT: A 356 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8405 (tttt) REVERT: S 93 GLU cc_start: 0.8274 (tt0) cc_final: 0.8004 (mt-10) REVERT: B 305 LYS cc_start: 0.8318 (mptp) cc_final: 0.7881 (mmpt) REVERT: B 356 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8404 (tttt) REVERT: C 93 GLU cc_start: 0.8340 (tt0) cc_final: 0.8058 (mt-10) REVERT: D 305 LYS cc_start: 0.8372 (mptp) cc_final: 0.7917 (mmpt) REVERT: D 356 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8385 (tttt) REVERT: E 93 GLU cc_start: 0.8261 (tt0) cc_final: 0.8001 (mt-10) REVERT: F 305 LYS cc_start: 0.8360 (mptp) cc_final: 0.7907 (mmpt) REVERT: F 356 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8412 (tttt) REVERT: G 93 GLU cc_start: 0.8265 (tt0) cc_final: 0.7993 (mt-10) REVERT: H 305 LYS cc_start: 0.8337 (mptp) cc_final: 0.7895 (mmpt) REVERT: H 356 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8395 (tttt) REVERT: I 93 GLU cc_start: 0.8201 (tt0) cc_final: 0.7990 (mt-10) REVERT: J 305 LYS cc_start: 0.8344 (mptp) cc_final: 0.7906 (mmpt) REVERT: J 356 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8389 (tttt) REVERT: K 93 GLU cc_start: 0.8223 (tt0) cc_final: 0.7997 (mt-10) REVERT: L 305 LYS cc_start: 0.8378 (mptp) cc_final: 0.7924 (mmpt) REVERT: L 356 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8383 (tttt) REVERT: M 93 GLU cc_start: 0.8190 (tt0) cc_final: 0.7989 (mt-10) REVERT: N 305 LYS cc_start: 0.8380 (mptp) cc_final: 0.7923 (mmpt) REVERT: N 356 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8402 (tttt) REVERT: O 93 GLU cc_start: 0.8185 (tt0) cc_final: 0.7956 (mt-10) outliers start: 11 outliers final: 0 residues processed: 555 average time/residue: 0.8929 time to fit residues: 578.7306 Evaluate side-chains 505 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 196 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 306 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 357 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 48 HIS S 82 GLN S 96 ASN A C 48 HIS C 55 HIS C 82 GLN C 96 ASN A E 82 GLN E 96 ASN A G 48 HIS G 55 HIS G 82 GLN G 96 ASN A I 48 HIS I 82 GLN I 96 ASN A K 48 HIS K 55 HIS K 96 ASN A M 48 HIS M 82 GLN M 96 ASN A O 48 HIS O 82 GLN O 96 ASN A Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.179207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137096 restraints weight = 152425.268| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.53 r_work: 0.3046 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work: 0.2824 rms_B_bonded: 4.02 restraints_weight: 0.1250 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37476 Z= 0.202 Angle : 0.693 7.301 51208 Z= 0.369 Chirality : 0.045 0.170 5504 Planarity : 0.005 0.037 6656 Dihedral : 5.476 23.600 5232 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.74 (0.12), residues: 4696 helix: 1.77 (0.12), residues: 1784 sheet: -1.01 (0.16), residues: 760 loop : 0.09 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 253 TYR 0.018 0.002 TYR B 269 PHE 0.035 0.003 PHE D 345 TRP 0.008 0.001 TRP D 462 HIS 0.013 0.002 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (37472) covalent geometry : angle 0.69116 / 0.37 (51200) SS BOND : bond 0.01632 / 0.82 ( 4) SS BOND : angle 4.01660 / 1.80 ( 8) hydrogen bonds : bond 0.04886 / 3.29 ( 1672) hydrogen bonds : angle 6.33418 / 4.64 ( 4552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 520 time to evaluate : 1.398 Fit side-chains REVERT: A 305 LYS cc_start: 0.8381 (mptp) cc_final: 0.7872 (mmpt) REVERT: A 356 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8384 (tttt) REVERT: S 93 GLU cc_start: 0.8301 (tt0) cc_final: 0.8054 (mt-10) REVERT: B 305 LYS cc_start: 0.8379 (mptp) cc_final: 0.7867 (mmpt) REVERT: B 356 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8392 (tttt) REVERT: C 93 GLU cc_start: 0.8347 (tt0) cc_final: 0.8080 (mt-10) REVERT: D 305 LYS cc_start: 0.8446 (mptp) cc_final: 0.7910 (mmpt) REVERT: D 356 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8382 (tttt) REVERT: E 93 GLU cc_start: 0.8313 (tt0) cc_final: 0.8032 (mt-10) REVERT: F 250 MET cc_start: 0.9248 (ttp) cc_final: 0.8724 (ttp) REVERT: F 305 LYS cc_start: 0.8443 (mptp) cc_final: 0.7913 (mmpt) REVERT: F 356 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8393 (tttt) REVERT: G 93 GLU cc_start: 0.8279 (tt0) cc_final: 0.8016 (mt-10) REVERT: H 305 LYS cc_start: 0.8390 (mptp) cc_final: 0.7879 (mmpt) REVERT: H 356 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8388 (tttt) REVERT: J 305 LYS cc_start: 0.8407 (mptp) cc_final: 0.7891 (mmpt) REVERT: J 356 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8360 (tttt) REVERT: K 93 GLU cc_start: 0.8214 (tt0) cc_final: 0.7976 (mt-10) REVERT: L 305 LYS cc_start: 0.8449 (mptp) cc_final: 0.7915 (mmpt) REVERT: L 356 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8381 (tttt) REVERT: M 93 GLU cc_start: 0.8193 (tt0) cc_final: 0.7963 (mt-10) REVERT: N 250 MET cc_start: 0.9250 (ttp) cc_final: 0.8728 (ttp) REVERT: N 305 LYS cc_start: 0.8453 (mptp) cc_final: 0.7923 (mmpt) REVERT: N 356 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8385 (tttt) REVERT: O 93 GLU cc_start: 0.8188 (tt0) cc_final: 0.7936 (mt-10) outliers start: 4 outliers final: 0 residues processed: 524 average time/residue: 0.9932 time to fit residues: 607.6513 Evaluate side-chains 509 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 248 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 392 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 403 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN B S 55 HIS S 82 GLN B 401 GLN B C 82 GLN D 401 GLN B E 55 HIS E 82 GLN F 401 GLN B G 82 GLN H 401 GLN B I 55 HIS I 82 GLN J 401 GLN B L 401 GLN B M 55 HIS M 82 GLN N 401 GLN B O 55 HIS O 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.179032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137740 restraints weight = 157105.427| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.71 r_work: 0.3056 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.2888 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 : 0.006 0.060 37476 Z= 0.274 Angle : 0.785 9.370 51208 Z= 0.420 Chirality : 0.048 0.182 5504 Planarity : 0.006 0.054 6656 Dihedral : 5.648 24.162 5232 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.31 % Allowed : 7.45 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.57 (0.12), residues: 4696 helix: 1.61 (0.12), residues: 1800 sheet: -1.47 (0.15), residues: 664 loop : 0.07 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 253 TYR 0.026 0.003 TYR D 269 PHE 0.036 0.004 PHE D 345 TRP 0.011 0.002 TRP A 462 HIS 0.017 0.003 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 (37472) covalent geometry : angle 0.78298 / 0.42 (51200) SS BOND : bond 0.01933 / 0.97 ( 4) SS BOND : angle 4.52907 / 2.03 ( 8) hydrogen bonds : bond 0.05518 / 3.72 ( 1672) hydrogen bonds : angle 6.52861 / 4.77 ( 4552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 525 time to evaluate : 1.291 Fit side-chains REVERT: A 250 MET cc_start: 0.9253 (ttp) cc_final: 0.8818 (ttp) REVERT: A 305 LYS cc_start: 0.8383 (mptp) cc_final: 0.7972 (mmpt) REVERT: S 93 GLU cc_start: 0.8183 (tt0) cc_final: 0.7951 (mt-10) REVERT: B 250 MET cc_start: 0.9252 (ttp) cc_final: 0.8818 (ttp) REVERT: B 305 LYS cc_start: 0.8395 (mptp) cc_final: 0.7972 (mmpt) REVERT: C 93 GLU cc_start: 0.8225 (tt0) cc_final: 0.7980 (mt-10) REVERT: D 250 MET cc_start: 0.9255 (ttp) cc_final: 0.8824 (ttp) REVERT: D 305 LYS cc_start: 0.8437 (mptp) cc_final: 0.8000 (mmpt) REVERT: E 93 GLU cc_start: 0.8237 (tt0) cc_final: 0.8016 (mt-10) REVERT: F 250 MET cc_start: 0.9249 (ttp) cc_final: 0.8771 (ttp) REVERT: F 305 LYS cc_start: 0.8424 (mptp) cc_final: 0.7996 (mmpt) REVERT: G 93 GLU cc_start: 0.8177 (tt0) cc_final: 0.7941 (mt-10) REVERT: H 250 MET cc_start: 0.9254 (ttp) cc_final: 0.8822 (ttp) REVERT: H 305 LYS cc_start: 0.8381 (mptp) cc_final: 0.7958 (mmpt) REVERT: J 250 MET cc_start: 0.9251 (ttp) cc_final: 0.8814 (ttp) REVERT: J 305 LYS cc_start: 0.8403 (mptp) cc_final: 0.7983 (mmpt) REVERT: K 93 GLU cc_start: 0.8143 (tt0) cc_final: 0.7912 (mt-10) REVERT: L 250 MET cc_start: 0.9256 (ttp) cc_final: 0.8830 (ttp) REVERT: L 305 LYS cc_start: 0.8432 (mptp) cc_final: 0.8003 (mmpt) REVERT: M 93 GLU cc_start: 0.8168 (tt0) cc_final: 0.7913 (mt-10) REVERT: N 250 MET cc_start: 0.9251 (ttp) cc_final: 0.8777 (ttp) REVERT: N 305 LYS cc_start: 0.8436 (mptp) cc_final: 0.8012 (mmpt) REVERT: O 93 GLU cc_start: 0.8123 (tt0) cc_final: 0.7881 (mt-10) outliers start: 4 outliers final: 0 residues processed: 527 average time/residue: 1.0108 time to fit residues: 620.3540 Evaluate side-chains 513 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 120 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN C 82 GLN E 82 GLN G 82 GLN I 82 GLN M 82 GLN O 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.178033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.135902 restraints weight = 162572.959| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.54 r_work: 0.3136 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work: 0.2963 rms_B_bonded: 3.71 restraints_weight: 0.1250 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37476 Z= 0.219 Angle : 0.708 7.983 51208 Z= 0.377 Chirality : 0.045 0.178 5504 Planarity : 0.005 0.038 6656 Dihedral : 5.483 23.871 5232 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.62 % Allowed : 8.20 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.70 (0.12), residues: 4696 helix: 1.74 (0.12), residues: 1792 sheet: -1.47 (0.15), residues: 664 loop : 0.16 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 253 TYR 0.021 0.003 TYR B 269 PHE 0.034 0.003 PHE D 345 TRP 0.009 0.001 TRP D 462 HIS 0.016 0.002 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (37472) covalent geometry : angle 0.70648 / 0.38 (51200) SS BOND : bond 0.01706 / 0.85 ( 4) SS BOND : angle 3.70759 / 1.66 ( 8) hydrogen bonds : bond 0.04953 / 3.34 ( 1672) hydrogen bonds : angle 6.37478 / 4.67 ( 4552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 528 time to evaluate : 1.367 Fit side-chains REVERT: A 250 MET cc_start: 0.9234 (ttp) cc_final: 0.8758 (ttp) REVERT: A 305 LYS cc_start: 0.8439 (mptp) cc_final: 0.7986 (mmpt) REVERT: S 93 GLU cc_start: 0.8214 (tt0) cc_final: 0.7950 (mt-10) REVERT: B 250 MET cc_start: 0.9236 (ttp) cc_final: 0.8759 (ttp) REVERT: B 305 LYS cc_start: 0.8434 (mptp) cc_final: 0.7987 (mmpt) REVERT: C 93 GLU cc_start: 0.8238 (tt0) cc_final: 0.7964 (mt-10) REVERT: D 250 MET cc_start: 0.9238 (ttp) cc_final: 0.8767 (ttp) REVERT: D 305 LYS cc_start: 0.8502 (mptp) cc_final: 0.8019 (mmpt) REVERT: E 93 GLU cc_start: 0.8214 (tt0) cc_final: 0.7970 (mt-10) REVERT: F 305 LYS cc_start: 0.8464 (mptp) cc_final: 0.8002 (mmpt) REVERT: G 93 GLU cc_start: 0.8214 (tt0) cc_final: 0.7954 (mt-10) REVERT: H 250 MET cc_start: 0.9238 (ttp) cc_final: 0.8763 (ttp) REVERT: H 305 LYS cc_start: 0.8445 (mptp) cc_final: 0.7992 (mmpt) REVERT: J 250 MET cc_start: 0.9235 (ttp) cc_final: 0.8757 (ttp) REVERT: J 305 LYS cc_start: 0.8444 (mptp) cc_final: 0.8001 (mmpt) REVERT: K 93 GLU cc_start: 0.8173 (tt0) cc_final: 0.7966 (mt-10) REVERT: L 250 MET cc_start: 0.9242 (ttp) cc_final: 0.8771 (ttp) REVERT: L 305 LYS cc_start: 0.8462 (mptp) cc_final: 0.7997 (mmpt) REVERT: M 93 GLU cc_start: 0.8176 (tt0) cc_final: 0.7965 (mt-10) REVERT: N 305 LYS cc_start: 0.8473 (mptp) cc_final: 0.8006 (mmpt) REVERT: O 93 GLU cc_start: 0.8144 (tt0) cc_final: 0.7932 (mt-10) outliers start: 12 outliers final: 0 residues processed: 534 average time/residue: 0.9771 time to fit residues: 608.7224 Evaluate side-chains 518 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 177 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 251 optimal weight: 30.0000 chunk 179 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN C 82 GLN E 82 GLN G 82 GLN I 82 GLN M 82 GLN O 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.178579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.136892 restraints weight = 161353.782| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.54 r_work: 0.3143 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.2976 rms_B_bonded: 3.62 restraints_weight: 0.1250 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37476 Z= 0.205 Angle : 0.689 7.831 51208 Z= 0.367 Chirality : 0.045 0.178 5504 Planarity : 0.005 0.036 6656 Dihedral : 5.414 23.814 5232 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.49 % Allowed : 8.43 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.75 (0.12), residues: 4696 helix: 1.81 (0.12), residues: 1792 sheet: -1.48 (0.15), residues: 664 loop : 0.17 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 253 TYR 0.020 0.002 TYR F 269 PHE 0.034 0.003 PHE D 345 TRP 0.008 0.001 TRP N 462 HIS 0.016 0.002 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (37472) covalent geometry : angle 0.68752 / 0.37 (51200) SS BOND : bond 0.01657 / 0.83 ( 4) SS BOND : angle 3.54355 / 1.59 ( 8) hydrogen bonds : bond 0.04807 / 3.24 ( 1672) hydrogen bonds : angle 6.32026 / 4.63 ( 4552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 1.495 Fit side-chains REVERT: A 305 LYS cc_start: 0.8429 (mptp) cc_final: 0.8008 (mmpt) REVERT: S 93 GLU cc_start: 0.8192 (tt0) cc_final: 0.7936 (mt-10) REVERT: B 250 MET cc_start: 0.9234 (ttp) cc_final: 0.8793 (ttp) REVERT: B 305 LYS cc_start: 0.8429 (mptp) cc_final: 0.8006 (mmpt) REVERT: C 93 GLU cc_start: 0.8223 (tt0) cc_final: 0.7980 (mt-10) REVERT: D 305 LYS cc_start: 0.8487 (mptp) cc_final: 0.8019 (mmpt) REVERT: E 93 GLU cc_start: 0.8185 (tt0) cc_final: 0.7898 (mt-10) REVERT: F 305 LYS cc_start: 0.8475 (mptp) cc_final: 0.8005 (mmpt) REVERT: G 93 GLU cc_start: 0.8190 (tt0) cc_final: 0.7923 (mt-10) REVERT: H 305 LYS cc_start: 0.8436 (mptp) cc_final: 0.8010 (mmpt) REVERT: J 305 LYS cc_start: 0.8445 (mptp) cc_final: 0.8032 (mmpt) REVERT: K 93 GLU cc_start: 0.8138 (tt0) cc_final: 0.7909 (mt-10) REVERT: L 250 MET cc_start: 0.9245 (ttp) cc_final: 0.8813 (ttp) REVERT: L 305 LYS cc_start: 0.8476 (mptp) cc_final: 0.8022 (mmpt) REVERT: M 93 GLU cc_start: 0.8144 (tt0) cc_final: 0.7903 (mt-10) REVERT: N 305 LYS cc_start: 0.8472 (mptp) cc_final: 0.8020 (mmpt) REVERT: O 93 GLU cc_start: 0.8117 (tt0) cc_final: 0.7902 (mt-10) outliers start: 3 outliers final: 2 residues processed: 537 average time/residue: 1.0076 time to fit residues: 630.8473 Evaluate side-chains 519 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 276 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 HIS S 82 GLN C 82 GLN E 82 GLN G 82 GLN H 282 HIS I 82 GLN M 82 GLN O 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.178001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.135778 restraints weight = 150962.740| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.64 r_work: 0.3122 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work: 0.2954 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37476 Z= 0.234 Angle : 0.727 8.507 51208 Z= 0.388 Chirality : 0.046 0.181 5504 Planarity : 0.005 0.044 6656 Dihedral : 5.472 23.924 5232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.54 % Allowed : 8.63 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.12), residues: 4696 helix: 1.74 (0.12), residues: 1800 sheet: -1.47 (0.15), residues: 664 loop : 0.13 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 253 TYR 0.023 0.003 TYR L 269 PHE 0.034 0.004 PHE D 345 TRP 0.009 0.002 TRP N 462 HIS 0.017 0.002 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (37472) covalent geometry : angle 0.72514 / 0.39 (51200) SS BOND : bond 0.01804 / 0.90 ( 4) SS BOND : angle 3.85405 / 1.73 ( 8) hydrogen bonds : bond 0.05060 / 3.41 ( 1672) hydrogen bonds : angle 6.39766 / 4.68 ( 4552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 523 time to evaluate : 1.069 Fit side-chains REVERT: A 250 MET cc_start: 0.9245 (ttp) cc_final: 0.8811 (ttp) REVERT: A 305 LYS cc_start: 0.8436 (mptp) cc_final: 0.8006 (mmpt) REVERT: S 93 GLU cc_start: 0.8220 (tt0) cc_final: 0.7956 (mt-10) REVERT: B 250 MET cc_start: 0.9244 (ttp) cc_final: 0.8807 (ttp) REVERT: B 305 LYS cc_start: 0.8423 (mptp) cc_final: 0.7997 (mmpt) REVERT: C 93 GLU cc_start: 0.8291 (tt0) cc_final: 0.8043 (mt-10) REVERT: D 250 MET cc_start: 0.9249 (ttp) cc_final: 0.8818 (ttp) REVERT: D 305 LYS cc_start: 0.8489 (mptp) cc_final: 0.8030 (mmpt) REVERT: E 93 GLU cc_start: 0.8201 (tt0) cc_final: 0.7938 (mt-10) REVERT: F 250 MET cc_start: 0.9246 (ttp) cc_final: 0.8819 (ttp) REVERT: F 305 LYS cc_start: 0.8477 (mptp) cc_final: 0.8006 (mmpt) REVERT: G 93 GLU cc_start: 0.8217 (tt0) cc_final: 0.7950 (mt-10) REVERT: H 250 MET cc_start: 0.9248 (ttp) cc_final: 0.8821 (ttp) REVERT: H 305 LYS cc_start: 0.8437 (mptp) cc_final: 0.8010 (mmpt) REVERT: J 250 MET cc_start: 0.9247 (ttp) cc_final: 0.8817 (ttp) REVERT: J 305 LYS cc_start: 0.8447 (mptp) cc_final: 0.8024 (mmpt) REVERT: K 93 GLU cc_start: 0.8179 (tt0) cc_final: 0.7934 (mt-10) REVERT: L 250 MET cc_start: 0.9251 (ttp) cc_final: 0.8824 (ttp) REVERT: L 305 LYS cc_start: 0.8470 (mptp) cc_final: 0.8009 (mmpt) REVERT: M 93 GLU cc_start: 0.8184 (tt0) cc_final: 0.7940 (mt-10) REVERT: N 250 MET cc_start: 0.9246 (ttp) cc_final: 0.8824 (ttp) REVERT: N 305 LYS cc_start: 0.8491 (mptp) cc_final: 0.8027 (mmpt) REVERT: O 93 GLU cc_start: 0.8155 (tt0) cc_final: 0.7940 (mt-10) outliers start: 5 outliers final: 3 residues processed: 526 average time/residue: 0.9555 time to fit residues: 583.8970 Evaluate side-chains 522 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 519 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain M residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 137 optimal weight: 1.9990 chunk 386 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN C 82 GLN E 82 GLN G 82 GLN I 82 GLN M 82 GLN N 282 HIS O 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.178054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136413 restraints weight = 158709.495| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.54 r_work: 0.3127 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.2956 rms_B_bonded: 3.63 restraints_weight: 0.1250 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 37476 Z= 0.232 Angle : 0.721 8.181 51208 Z= 0.385 Chirality : 0.046 0.182 5504 Planarity : 0.005 0.041 6656 Dihedral : 5.456 23.924 5232 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.59 % Allowed : 8.58 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.12), residues: 4696 helix: 1.73 (0.12), residues: 1800 sheet: -1.48 (0.15), residues: 664 loop : 0.14 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 253 TYR 0.023 0.003 TYR D 269 PHE 0.033 0.004 PHE D 345 TRP 0.009 0.002 TRP N 462 HIS 0.017 0.002 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (37472) covalent geometry : angle 0.71936 / 0.38 (51200) SS BOND : bond 0.01774 / 0.89 ( 4) SS BOND : angle 3.71368 / 1.66 ( 8) hydrogen bonds : bond 0.05022 / 3.39 ( 1672) hydrogen bonds : angle 6.39564 / 4.68 ( 4552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 525 time to evaluate : 1.301 Fit side-chains REVERT: A 250 MET cc_start: 0.9240 (ttp) cc_final: 0.8795 (ttp) REVERT: A 305 LYS cc_start: 0.8430 (mptp) cc_final: 0.8012 (mmpt) REVERT: S 93 GLU cc_start: 0.8174 (tt0) cc_final: 0.7908 (mt-10) REVERT: B 250 MET cc_start: 0.9239 (ttp) cc_final: 0.8794 (ttp) REVERT: B 305 LYS cc_start: 0.8416 (mptp) cc_final: 0.7997 (mmpt) REVERT: C 93 GLU cc_start: 0.8255 (tt0) cc_final: 0.8004 (mt-10) REVERT: D 250 MET cc_start: 0.9244 (ttp) cc_final: 0.8806 (ttp) REVERT: D 305 LYS cc_start: 0.8475 (mptp) cc_final: 0.8017 (mmpt) REVERT: E 93 GLU cc_start: 0.8176 (tt0) cc_final: 0.7888 (mt-10) REVERT: F 250 MET cc_start: 0.9241 (ttp) cc_final: 0.8814 (ttp) REVERT: F 305 LYS cc_start: 0.8449 (mptp) cc_final: 0.7983 (mmpt) REVERT: G 93 GLU cc_start: 0.8180 (tt0) cc_final: 0.7912 (mt-10) REVERT: H 250 MET cc_start: 0.9244 (ttp) cc_final: 0.8810 (ttp) REVERT: H 305 LYS cc_start: 0.8434 (mptp) cc_final: 0.8020 (mmpt) REVERT: J 250 MET cc_start: 0.9242 (ttp) cc_final: 0.8800 (ttp) REVERT: J 305 LYS cc_start: 0.8423 (mptp) cc_final: 0.8015 (mmpt) REVERT: K 93 GLU cc_start: 0.8140 (tt0) cc_final: 0.7892 (mt-10) REVERT: L 250 MET cc_start: 0.9247 (ttp) cc_final: 0.8811 (ttp) REVERT: L 305 LYS cc_start: 0.8446 (mptp) cc_final: 0.7988 (mmpt) REVERT: M 93 GLU cc_start: 0.8149 (tt0) cc_final: 0.7906 (mt-10) REVERT: N 250 MET cc_start: 0.9241 (ttp) cc_final: 0.8815 (ttp) REVERT: N 305 LYS cc_start: 0.8474 (mptp) cc_final: 0.8016 (mmpt) REVERT: O 93 GLU cc_start: 0.8125 (tt0) cc_final: 0.7908 (mt-10) outliers start: 8 outliers final: 6 residues processed: 527 average time/residue: 0.9390 time to fit residues: 574.8855 Evaluate side-chains 529 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 523 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain O residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 283 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN C 82 GLN E 82 GLN G 82 GLN I 82 GLN M 82 GLN O 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.177999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.136320 restraints weight = 159091.248| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.55 r_work: 0.3126 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.2958 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37476 Z= 0.234 Angle : 0.727 8.342 51208 Z= 0.388 Chirality : 0.046 0.182 5504 Planarity : 0.005 0.042 6656 Dihedral : 5.462 23.910 5232 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.49 % Allowed : 8.74 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.12), residues: 4696 helix: 1.73 (0.12), residues: 1800 sheet: -1.49 (0.15), residues: 664 loop : 0.14 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 253 TYR 0.023 0.003 TYR B 269 PHE 0.033 0.004 PHE D 345 TRP 0.008 0.002 TRP N 462 HIS 0.017 0.002 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (37472) covalent geometry : angle 0.72525 / 0.39 (51200) SS BOND : bond 0.01779 / 0.89 ( 4) SS BOND : angle 3.76577 / 1.69 ( 8) hydrogen bonds : bond 0.05044 / 3.40 ( 1672) hydrogen bonds : angle 6.40228 / 4.69 ( 4552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 531 time to evaluate : 1.322 Fit side-chains REVERT: A 250 MET cc_start: 0.9241 (ttp) cc_final: 0.8797 (ttp) REVERT: A 305 LYS cc_start: 0.8427 (mptp) cc_final: 0.8013 (mmpt) REVERT: S 93 GLU cc_start: 0.8177 (tt0) cc_final: 0.7912 (mt-10) REVERT: B 250 MET cc_start: 0.9238 (ttp) cc_final: 0.8792 (ttp) REVERT: B 305 LYS cc_start: 0.8391 (mptp) cc_final: 0.7975 (mmpt) REVERT: C 93 GLU cc_start: 0.8264 (tt0) cc_final: 0.8016 (mt-10) REVERT: D 250 MET cc_start: 0.9246 (ttp) cc_final: 0.8807 (ttp) REVERT: D 305 LYS cc_start: 0.8474 (mptp) cc_final: 0.8020 (mmpt) REVERT: E 93 GLU cc_start: 0.8188 (tt0) cc_final: 0.7921 (mt-10) REVERT: F 250 MET cc_start: 0.9240 (ttp) cc_final: 0.8813 (ttp) REVERT: F 305 LYS cc_start: 0.8452 (mptp) cc_final: 0.7982 (mmpt) REVERT: G 93 GLU cc_start: 0.8181 (tt0) cc_final: 0.7918 (mt-10) REVERT: H 250 MET cc_start: 0.9243 (ttp) cc_final: 0.8808 (ttp) REVERT: H 305 LYS cc_start: 0.8414 (mptp) cc_final: 0.7998 (mmpt) REVERT: J 250 MET cc_start: 0.9243 (ttp) cc_final: 0.8803 (ttp) REVERT: J 305 LYS cc_start: 0.8438 (mptp) cc_final: 0.8031 (mmpt) REVERT: K 93 GLU cc_start: 0.8159 (tt0) cc_final: 0.7913 (mt-10) REVERT: L 250 MET cc_start: 0.9247 (ttp) cc_final: 0.8808 (ttp) REVERT: L 305 LYS cc_start: 0.8446 (mptp) cc_final: 0.7989 (mmpt) REVERT: M 93 GLU cc_start: 0.8148 (tt0) cc_final: 0.7905 (mt-10) REVERT: N 250 MET cc_start: 0.9242 (ttp) cc_final: 0.8816 (ttp) REVERT: N 305 LYS cc_start: 0.8464 (mptp) cc_final: 0.8009 (mmpt) REVERT: O 93 GLU cc_start: 0.8136 (tt0) cc_final: 0.7921 (mt-10) outliers start: 6 outliers final: 6 residues processed: 531 average time/residue: 0.9097 time to fit residues: 562.1567 Evaluate side-chains 531 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 525 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain O residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 187 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 306 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 300 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN C 82 GLN E 82 GLN G 82 GLN I 82 GLN M 82 GLN O 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.137282 restraints weight = 149779.885| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.69 r_work: 0.3140 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.2977 rms_B_bonded: 3.61 restraints_weight: 0.1250 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37476 Z= 0.196 Angle : 0.678 7.285 51208 Z= 0.362 Chirality : 0.044 0.178 5504 Planarity : 0.005 0.031 6656 Dihedral : 5.355 23.675 5232 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.41 % Allowed : 8.89 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 4696 helix: 1.85 (0.12), residues: 1792 sheet: -1.47 (0.15), residues: 664 loop : 0.21 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 350 TYR 0.019 0.002 TYR L 269 PHE 0.032 0.003 PHE D 345 TRP 0.008 0.001 TRP B 462 HIS 0.016 0.002 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (37472) covalent geometry : angle 0.67679 / 0.36 (51200) SS BOND : bond 0.01615 / 0.81 ( 4) SS BOND : angle 3.37164 / 1.51 ( 8) hydrogen bonds : bond 0.04677 / 3.15 ( 1672) hydrogen bonds : angle 6.29997 / 4.61 ( 4552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 533 time to evaluate : 1.242 Fit side-chains REVERT: A 305 LYS cc_start: 0.8415 (mptp) cc_final: 0.7987 (mmpt) REVERT: S 93 GLU cc_start: 0.8151 (tt0) cc_final: 0.7872 (mt-10) REVERT: B 305 LYS cc_start: 0.8432 (mptp) cc_final: 0.7997 (mmpt) REVERT: C 93 GLU cc_start: 0.8209 (tt0) cc_final: 0.7957 (mt-10) REVERT: D 305 LYS cc_start: 0.8454 (mptp) cc_final: 0.7981 (mmpt) REVERT: E 93 GLU cc_start: 0.8175 (tt0) cc_final: 0.7873 (mt-10) REVERT: F 305 LYS cc_start: 0.8450 (mptp) cc_final: 0.7951 (mmpt) REVERT: G 93 GLU cc_start: 0.8154 (tt0) cc_final: 0.7876 (mt-10) REVERT: H 305 LYS cc_start: 0.8421 (mptp) cc_final: 0.7995 (mmpt) REVERT: J 305 LYS cc_start: 0.8442 (mptp) cc_final: 0.8027 (mmpt) REVERT: K 93 GLU cc_start: 0.8122 (tt0) cc_final: 0.7867 (mt-10) REVERT: L 305 LYS cc_start: 0.8435 (mptp) cc_final: 0.7944 (mmpt) REVERT: M 93 GLU cc_start: 0.8129 (tt0) cc_final: 0.7871 (mt-10) REVERT: N 250 MET cc_start: 0.9227 (ttp) cc_final: 0.8820 (ttp) REVERT: N 305 LYS cc_start: 0.8456 (mptp) cc_final: 0.7960 (mmpt) REVERT: O 93 GLU cc_start: 0.8086 (tt0) cc_final: 0.7859 (mt-10) outliers start: 6 outliers final: 6 residues processed: 533 average time/residue: 0.9463 time to fit residues: 587.0974 Evaluate side-chains 531 residues out of total 3488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 525 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain O residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 303 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN B 282 HIS C 82 GLN D 282 HIS E 82 GLN F 282 HIS G 82 GLN I 82 GLN J 282 HIS L 282 HIS M 82 GLN O 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.134682 restraints weight = 148750.459| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.59 r_work: 0.3105 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work: 0.2922 rms_B_bonded: 3.97 restraints_weight: 0.1250 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 37476 Z= 0.315 Angle : 0.831 10.210 51208 Z= 0.447 Chirality : 0.049 0.188 5504 Planarity : 0.006 0.063 6656 Dihedral : 5.643 24.286 5232 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.41 % Allowed : 9.02 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.57 (0.12), residues: 4696 helix: 1.55 (0.12), residues: 1800 sheet: -1.48 (0.15), residues: 664 loop : 0.13 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 213 TYR 0.031 0.004 TYR D 269 PHE 0.035 0.004 PHE D 345 TRP 0.010 0.002 TRP B 214 HIS 0.016 0.003 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.32 (37472) covalent geometry : angle 0.82933 / 0.45 (51200) SS BOND : bond 0.02095 / 1.05 ( 4) SS BOND : angle 4.44319 / 1.99 ( 8) hydrogen bonds : bond 0.05701 / 3.84 ( 1672) hydrogen bonds : angle 6.58995 / 4.82 ( 4552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26626.65 seconds wall clock time: 452 minutes 21.84 seconds (27141.84 seconds total)