Starting phenix.real_space_refine on Sun Sep 29 03:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/09_2024/8f0u_28781.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.203 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: 5 Type Number sf(0) Gaussians S 168 5.16 5 C 22188 2.51 5 N 6264 2.21 5 O 6864 1.98 5 H 36756 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72240 Number of models: 1 Model: "" Number of chains: 3 Chain: "0" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "1" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: 4, 7, C, D, G, J, M, P, S, V, Y, 3, 6, A, B, F, I, L, O, R, U, X, 5, 8, E, H, K, N, Q, T, W, Z, a Time building chain proxies: 14.02, per 1000 atoms: 0.19 Number of scatterers: 72240 At special positions: 0 Unit cell: (170.66, 164.3, 155.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 O 6864 8.00 N 6264 7.00 C 22188 6.00 H 36756 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 4.4 seconds 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8712 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 84 sheets defined 23.3% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.37 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'a' and resid 37 through 49 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 24 Proline residue: B 24 - end of helix No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 21 through 24 Proline residue: F 24 - end of helix No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 280 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'G' and resid 394 through 399 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'I' and resid 15 through 20 Processing helix chain 'I' and resid 21 through 24 Proline residue: I 24 - end of helix No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 154 through 158 Processing helix chain 'I' and resid 169 through 173 Processing helix chain 'I' and resid 244 through 258 removed outlier: 3.611A pdb=" N GLN I 253 " --> pdb=" O ASN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 280 Processing helix chain 'I' and resid 297 through 303 Processing helix chain 'I' and resid 320 through 329 Processing helix chain 'J' and resid 394 through 399 Processing helix chain 'J' and resid 417 through 426 Processing helix chain 'K' and resid 37 through 49 Processing helix chain 'L' and resid 15 through 20 Processing helix chain 'L' and resid 21 through 24 Proline residue: L 24 - end of helix No H-bonds generated for 'chain 'L' and resid 21 through 24' Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 154 through 158 Processing helix chain 'L' and resid 169 through 173 Processing helix chain 'L' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN L 253 " --> pdb=" O ASN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 280 Processing helix chain 'L' and resid 297 through 303 Processing helix chain 'L' and resid 320 through 329 Processing helix chain 'M' and resid 394 through 399 Processing helix chain 'M' and resid 417 through 426 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'O' and resid 15 through 20 Processing helix chain 'O' and resid 21 through 24 Proline residue: O 24 - end of helix No H-bonds generated for 'chain 'O' and resid 21 through 24' Processing helix chain 'O' and resid 104 through 108 Processing helix chain 'O' and resid 154 through 158 Processing helix chain 'O' and resid 169 through 173 Processing helix chain 'O' and resid 244 through 258 removed outlier: 3.613A pdb=" N GLN O 253 " --> pdb=" O ASN O 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 280 Processing helix chain 'O' and resid 297 through 303 Processing helix chain 'O' and resid 320 through 329 Processing helix chain 'P' and resid 394 through 399 Processing helix chain 'P' and resid 417 through 426 Processing helix chain 'Q' and resid 37 through 49 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 21 through 24 Proline residue: R 24 - end of helix No H-bonds generated for 'chain 'R' and resid 21 through 24' Processing helix chain 'R' and resid 104 through 108 Processing helix chain 'R' and resid 154 through 158 Processing helix chain 'R' and resid 169 through 173 Processing helix chain 'R' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN R 253 " --> pdb=" O ASN R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 280 Processing helix chain 'R' and resid 297 through 303 Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'S' and resid 394 through 399 Processing helix chain 'S' and resid 417 through 426 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'U' and resid 15 through 20 Processing helix chain 'U' and resid 21 through 24 Proline residue: U 24 - end of helix No H-bonds generated for 'chain 'U' and resid 21 through 24' Processing helix chain 'U' and resid 104 through 108 Processing helix chain 'U' and resid 154 through 158 Processing helix chain 'U' and resid 169 through 173 Processing helix chain 'U' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN U 253 " --> pdb=" O ASN U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 280 Processing helix chain 'U' and resid 297 through 303 Processing helix chain 'U' and resid 320 through 329 Processing helix chain 'V' and resid 394 through 399 Processing helix chain 'V' and resid 417 through 426 Processing helix chain 'W' and resid 37 through 49 Processing helix chain 'X' and resid 15 through 20 Processing helix chain 'X' and resid 21 through 24 Proline residue: X 24 - end of helix No H-bonds generated for 'chain 'X' and resid 21 through 24' Processing helix chain 'X' and resid 104 through 108 Processing helix chain 'X' and resid 154 through 158 Processing helix chain 'X' and resid 169 through 173 Processing helix chain 'X' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN X 253 " --> pdb=" O ASN X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 280 Processing helix chain 'X' and resid 297 through 303 Processing helix chain 'X' and resid 320 through 329 Processing helix chain 'Y' and resid 394 through 399 Processing helix chain 'Y' and resid 417 through 426 Processing helix chain 'Z' and resid 37 through 49 Processing helix chain '0' and resid 15 through 20 Processing helix chain '0' and resid 21 through 24 Proline residue: 0 24 - end of helix No H-bonds generated for 'chain '0' and resid 21 through 24' Processing helix chain '0' and resid 104 through 108 Processing helix chain '0' and resid 154 through 158 Processing helix chain '0' and resid 169 through 173 Processing helix chain '0' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN 0 253 " --> pdb=" O ASN 0 249 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 280 Processing helix chain '0' and resid 297 through 303 Processing helix chain '0' and resid 320 through 329 Processing helix chain '1' and resid 394 through 399 Processing helix chain '1' and resid 417 through 426 Processing helix chain '2' and resid 37 through 49 Processing helix chain '3' and resid 15 through 20 Processing helix chain '3' and resid 21 through 24 Proline residue: 3 24 - end of helix No H-bonds generated for 'chain '3' and resid 21 through 24' Processing helix chain '3' and resid 104 through 108 Processing helix chain '3' and resid 154 through 158 Processing helix chain '3' and resid 169 through 173 Processing helix chain '3' and resid 244 through 258 removed outlier: 3.611A pdb=" N GLN 3 253 " --> pdb=" O ASN 3 249 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 280 Processing helix chain '3' and resid 297 through 303 Processing helix chain '3' and resid 320 through 329 Processing helix chain '4' and resid 394 through 399 Processing helix chain '4' and resid 417 through 426 Processing helix chain '5' and resid 37 through 49 Processing helix chain '6' and resid 15 through 20 Processing helix chain '6' and resid 21 through 24 Proline residue: 6 24 - end of helix No H-bonds generated for 'chain '6' and resid 21 through 24' Processing helix chain '6' and resid 104 through 108 Processing helix chain '6' and resid 154 through 158 Processing helix chain '6' and resid 169 through 173 Processing helix chain '6' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN 6 253 " --> pdb=" O ASN 6 249 " (cutoff:3.500A) Processing helix chain '6' and resid 273 through 280 Processing helix chain '6' and resid 297 through 303 Processing helix chain '6' and resid 320 through 329 Processing helix chain '7' and resid 394 through 399 Processing helix chain '7' and resid 417 through 426 Processing helix chain '8' and resid 37 through 49 Processing sheet with id=1, first strand: chain 'a' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET A 85 " --> pdb=" O PHE a 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER A 89 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A 103 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 99 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 136 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 130 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 138 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 113 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET A 127 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR A 111 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU A 32 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 113 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 30 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 115 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 28 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'a' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN A 225 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 242 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 200 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 185 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 214 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=4, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 340 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR A 338 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN D 435 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 410 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 433 " --> pdb=" O ALA D 410 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.252A pdb=" N MET B 85 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER B 89 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN B 103 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 99 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 136 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS B 130 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 138 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 113 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET B 127 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR B 111 " --> pdb=" O MET B 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU B 32 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 113 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 30 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 115 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER B 28 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN B 225 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE B 242 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN B 200 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 185 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 214 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=11, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY B 340 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 313 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B 338 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU C 375 " --> pdb=" O ASN C 388 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU C 375 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C 435 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA C 410 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA C 433 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET F 85 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER F 89 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN F 103 " --> pdb=" O SER F 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR F 99 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE F 136 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS F 130 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 138 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 113 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET F 127 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR F 111 " --> pdb=" O MET F 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU F 32 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE F 113 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN F 30 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL F 115 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER F 28 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN F 225 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE F 242 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN F 200 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU F 185 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU F 214 " --> pdb=" O ILE F 222 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=18, first strand: chain 'F' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET F 268 " --> pdb=" O SER F 291 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET F 268 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY F 340 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU F 313 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR F 338 " --> pdb=" O LEU F 313 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'G' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU G 375 " --> pdb=" O ASN G 388 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU G 375 " --> pdb=" O ASN G 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN G 435 " --> pdb=" O ILE G 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA G 410 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA G 433 " --> pdb=" O ALA G 410 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET I 85 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER I 89 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN I 103 " --> pdb=" O SER I 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR I 99 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE I 136 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS I 130 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU I 138 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE I 113 " --> pdb=" O ALA I 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET I 127 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR I 111 " --> pdb=" O MET I 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU I 32 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE I 113 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN I 30 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL I 115 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER I 28 " --> pdb=" O VAL I 115 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'K' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN I 225 " --> pdb=" O ILE I 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE I 242 " --> pdb=" O ASN I 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN I 200 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU I 185 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU I 214 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 263 through 264 Processing sheet with id=25, first strand: chain 'I' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET I 268 " --> pdb=" O SER I 291 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'I' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET I 268 " --> pdb=" O SER I 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY I 340 " --> pdb=" O THR I 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU I 313 " --> pdb=" O THR I 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR I 338 " --> pdb=" O LEU I 313 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'J' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU J 375 " --> pdb=" O ASN J 388 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'J' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU J 375 " --> pdb=" O ASN J 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN J 435 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA J 410 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA J 433 " --> pdb=" O ALA J 410 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'N' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET L 85 " --> pdb=" O PHE N 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER L 89 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN L 103 " --> pdb=" O SER L 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR L 99 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE L 136 " --> pdb=" O LYS L 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS L 130 " --> pdb=" O ILE L 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU L 138 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE L 113 " --> pdb=" O ALA L 125 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N MET L 127 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR L 111 " --> pdb=" O MET L 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU L 32 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE L 113 " --> pdb=" O ASN L 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN L 30 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL L 115 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER L 28 " --> pdb=" O VAL L 115 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'N' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN L 225 " --> pdb=" O ILE L 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE L 242 " --> pdb=" O ASN L 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN L 200 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU L 185 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU L 214 " --> pdb=" O ILE L 222 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'L' and resid 263 through 264 Processing sheet with id=32, first strand: chain 'L' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET L 268 " --> pdb=" O SER L 291 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'L' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET L 268 " --> pdb=" O SER L 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY L 340 " --> pdb=" O THR L 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU L 313 " --> pdb=" O THR L 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR L 338 " --> pdb=" O LEU L 313 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'M' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU M 375 " --> pdb=" O ASN M 388 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'M' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU M 375 " --> pdb=" O ASN M 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN M 435 " --> pdb=" O ILE M 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA M 410 " --> pdb=" O ALA M 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA M 433 " --> pdb=" O ALA M 410 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'Q' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET O 85 " --> pdb=" O PHE Q 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER O 89 " --> pdb=" O ASN O 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN O 103 " --> pdb=" O SER O 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR O 99 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE O 136 " --> pdb=" O LYS O 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS O 130 " --> pdb=" O ILE O 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU O 138 " --> pdb=" O VAL O 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE O 113 " --> pdb=" O ALA O 125 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N MET O 127 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR O 111 " --> pdb=" O MET O 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU O 32 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE O 113 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN O 30 " --> pdb=" O ILE O 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL O 115 " --> pdb=" O SER O 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER O 28 " --> pdb=" O VAL O 115 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'Q' and resid 29 through 31 removed outlier: 5.790A pdb=" N ASN O 225 " --> pdb=" O ILE O 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE O 242 " --> pdb=" O ASN O 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN O 200 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU O 185 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU O 214 " --> pdb=" O ILE O 222 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 263 through 264 Processing sheet with id=39, first strand: chain 'O' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET O 268 " --> pdb=" O SER O 291 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET O 268 " --> pdb=" O SER O 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY O 340 " --> pdb=" O THR O 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU O 313 " --> pdb=" O THR O 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR O 338 " --> pdb=" O LEU O 313 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'P' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU P 375 " --> pdb=" O ASN P 388 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'P' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU P 375 " --> pdb=" O ASN P 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN P 435 " --> pdb=" O ILE P 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA P 410 " --> pdb=" O ALA P 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA P 433 " --> pdb=" O ALA P 410 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'T' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET R 85 " --> pdb=" O PHE T 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER R 89 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN R 103 " --> pdb=" O SER R 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR R 99 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE R 136 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS R 130 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU R 138 " --> pdb=" O VAL R 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE R 113 " --> pdb=" O ALA R 125 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N MET R 127 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR R 111 " --> pdb=" O MET R 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU R 32 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE R 113 " --> pdb=" O ASN R 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN R 30 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL R 115 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER R 28 " --> pdb=" O VAL R 115 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'T' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN R 225 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE R 242 " --> pdb=" O ASN R 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN R 200 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU R 185 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU R 214 " --> pdb=" O ILE R 222 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'R' and resid 263 through 264 Processing sheet with id=46, first strand: chain 'R' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET R 268 " --> pdb=" O SER R 291 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'R' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET R 268 " --> pdb=" O SER R 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY R 340 " --> pdb=" O THR R 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU R 313 " --> pdb=" O THR R 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR R 338 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'S' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU S 375 " --> pdb=" O ASN S 388 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'S' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU S 375 " --> pdb=" O ASN S 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN S 435 " --> pdb=" O ILE S 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA S 410 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA S 433 " --> pdb=" O ALA S 410 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'W' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET U 85 " --> pdb=" O PHE W 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER U 89 " --> pdb=" O ASN U 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN U 103 " --> pdb=" O SER U 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR U 99 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE U 136 " --> pdb=" O LYS U 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS U 130 " --> pdb=" O ILE U 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU U 138 " --> pdb=" O VAL U 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE U 113 " --> pdb=" O ALA U 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET U 127 " --> pdb=" O THR U 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR U 111 " --> pdb=" O MET U 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU U 32 " --> pdb=" O THR U 111 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE U 113 " --> pdb=" O ASN U 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN U 30 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL U 115 " --> pdb=" O SER U 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER U 28 " --> pdb=" O VAL U 115 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'W' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN U 225 " --> pdb=" O ILE U 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE U 242 " --> pdb=" O ASN U 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN U 200 " --> pdb=" O LEU U 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU U 185 " --> pdb=" O GLN U 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU U 214 " --> pdb=" O ILE U 222 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'U' and resid 263 through 264 Processing sheet with id=53, first strand: chain 'U' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET U 268 " --> pdb=" O SER U 291 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'U' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET U 268 " --> pdb=" O SER U 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY U 340 " --> pdb=" O THR U 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU U 313 " --> pdb=" O THR U 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR U 338 " --> pdb=" O LEU U 313 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'V' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU V 375 " --> pdb=" O ASN V 388 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'V' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU V 375 " --> pdb=" O ASN V 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN V 435 " --> pdb=" O ILE V 408 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA V 410 " --> pdb=" O ALA V 433 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA V 433 " --> pdb=" O ALA V 410 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'Z' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET X 85 " --> pdb=" O PHE Z 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER X 89 " --> pdb=" O ASN X 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN X 103 " --> pdb=" O SER X 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR X 99 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE X 136 " --> pdb=" O LYS X 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS X 130 " --> pdb=" O ILE X 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU X 138 " --> pdb=" O VAL X 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE X 113 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET X 127 " --> pdb=" O THR X 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR X 111 " --> pdb=" O MET X 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU X 32 " --> pdb=" O THR X 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE X 113 " --> pdb=" O ASN X 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN X 30 " --> pdb=" O ILE X 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL X 115 " --> pdb=" O SER X 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER X 28 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'Z' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN X 225 " --> pdb=" O ILE X 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE X 242 " --> pdb=" O ASN X 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN X 200 " --> pdb=" O LEU X 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU X 185 " --> pdb=" O GLN X 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU X 214 " --> pdb=" O ILE X 222 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'X' and resid 263 through 264 Processing sheet with id=60, first strand: chain 'X' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET X 268 " --> pdb=" O SER X 291 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'X' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET X 268 " --> pdb=" O SER X 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY X 340 " --> pdb=" O THR X 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU X 313 " --> pdb=" O THR X 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR X 338 " --> pdb=" O LEU X 313 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'Y' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU Y 375 " --> pdb=" O ASN Y 388 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'Y' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU Y 375 " --> pdb=" O ASN Y 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN Y 435 " --> pdb=" O ILE Y 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA Y 410 " --> pdb=" O ALA Y 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA Y 433 " --> pdb=" O ALA Y 410 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain '2' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 0 85 " --> pdb=" O PHE 2 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER 0 89 " --> pdb=" O ASN 0 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN 0 103 " --> pdb=" O SER 0 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR 0 99 " --> pdb=" O ILE 0 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 0 136 " --> pdb=" O LYS 0 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS 0 130 " --> pdb=" O ILE 0 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 0 138 " --> pdb=" O VAL 0 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 0 113 " --> pdb=" O ALA 0 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET 0 127 " --> pdb=" O THR 0 111 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N THR 0 111 " --> pdb=" O MET 0 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU 0 32 " --> pdb=" O THR 0 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 0 113 " --> pdb=" O ASN 0 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 0 30 " --> pdb=" O ILE 0 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL 0 115 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER 0 28 " --> pdb=" O VAL 0 115 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain '2' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN 0 225 " --> pdb=" O ILE 0 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE 0 242 " --> pdb=" O ASN 0 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN 0 200 " --> pdb=" O LEU 0 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 0 185 " --> pdb=" O GLN 0 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 0 214 " --> pdb=" O ILE 0 222 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain '0' and resid 263 through 264 Processing sheet with id=67, first strand: chain '0' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 0 268 " --> pdb=" O SER 0 291 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain '0' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 0 268 " --> pdb=" O SER 0 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY 0 340 " --> pdb=" O THR 0 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 0 313 " --> pdb=" O THR 0 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 0 338 " --> pdb=" O LEU 0 313 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain '1' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU 1 375 " --> pdb=" O ASN 1 388 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain '1' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU 1 375 " --> pdb=" O ASN 1 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN 1 435 " --> pdb=" O ILE 1 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA 1 410 " --> pdb=" O ALA 1 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 1 433 " --> pdb=" O ALA 1 410 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain '5' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 3 85 " --> pdb=" O PHE 5 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER 3 89 " --> pdb=" O ASN 3 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN 3 103 " --> pdb=" O SER 3 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR 3 99 " --> pdb=" O ILE 3 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 3 136 " --> pdb=" O LYS 3 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS 3 130 " --> pdb=" O ILE 3 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 3 138 " --> pdb=" O VAL 3 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 3 113 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N MET 3 127 " --> pdb=" O THR 3 111 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N THR 3 111 " --> pdb=" O MET 3 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 3 32 " --> pdb=" O THR 3 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE 3 113 " --> pdb=" O ASN 3 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 3 30 " --> pdb=" O ILE 3 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL 3 115 " --> pdb=" O SER 3 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER 3 28 " --> pdb=" O VAL 3 115 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain '5' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN 3 225 " --> pdb=" O ILE 3 242 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE 3 242 " --> pdb=" O ASN 3 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN 3 200 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 3 185 " --> pdb=" O GLN 3 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 3 214 " --> pdb=" O ILE 3 222 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain '3' and resid 263 through 264 Processing sheet with id=74, first strand: chain '3' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 3 268 " --> pdb=" O SER 3 291 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain '3' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 3 268 " --> pdb=" O SER 3 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY 3 340 " --> pdb=" O THR 3 311 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU 3 313 " --> pdb=" O THR 3 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 3 338 " --> pdb=" O LEU 3 313 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain '4' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 4 375 " --> pdb=" O ASN 4 388 " (cutoff:3.500A) Processing sheet with id=77, first strand: chain '4' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 4 375 " --> pdb=" O ASN 4 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN 4 435 " --> pdb=" O ILE 4 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA 4 410 " --> pdb=" O ALA 4 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 4 433 " --> pdb=" O ALA 4 410 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain '8' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 6 85 " --> pdb=" O PHE 8 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER 6 89 " --> pdb=" O ASN 6 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN 6 103 " --> pdb=" O SER 6 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR 6 99 " --> pdb=" O ILE 6 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 6 136 " --> pdb=" O LYS 6 130 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS 6 130 " --> pdb=" O ILE 6 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 6 138 " --> pdb=" O VAL 6 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 6 113 " --> pdb=" O ALA 6 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET 6 127 " --> pdb=" O THR 6 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR 6 111 " --> pdb=" O MET 6 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 6 32 " --> pdb=" O THR 6 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 6 113 " --> pdb=" O ASN 6 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 6 30 " --> pdb=" O ILE 6 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL 6 115 " --> pdb=" O SER 6 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER 6 28 " --> pdb=" O VAL 6 115 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain '8' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN 6 225 " --> pdb=" O ILE 6 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE 6 242 " --> pdb=" O ASN 6 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN 6 200 " --> pdb=" O LEU 6 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 6 185 " --> pdb=" O GLN 6 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 6 214 " --> pdb=" O ILE 6 222 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain '6' and resid 263 through 264 Processing sheet with id=81, first strand: chain '6' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET 6 268 " --> pdb=" O SER 6 291 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain '6' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET 6 268 " --> pdb=" O SER 6 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY 6 340 " --> pdb=" O THR 6 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 6 313 " --> pdb=" O THR 6 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 6 338 " --> pdb=" O LEU 6 313 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain '7' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 7 375 " --> pdb=" O ASN 7 388 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain '7' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 7 375 " --> pdb=" O ASN 7 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN 7 435 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA 7 410 " --> pdb=" O ALA 7 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 7 433 " --> pdb=" O ALA 7 410 " (cutoff:3.500A) 1692 hydrogen bonds defined for protein. 4284 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: 34.10 Time building geometry restraints manager: 16.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 36756 1.13 - 1.30: 7039 1.30 - 1.48: 15032 1.48 - 1.65: 13401 1.65 - 1.83: 336 Bond restraints: 72564 Sorted by residual: bond pdb=" CB HIS 8 33 " pdb=" CG HIS 8 33 " ideal model delta sigma weight residual 1.497 1.339 0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CB HIS T 33 " pdb=" CG HIS T 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CB HIS N 33 " pdb=" CG HIS N 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS W 33 " pdb=" CG HIS W 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS E 33 " pdb=" CG HIS E 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 72559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 109964 2.41 - 4.83: 14507 4.83 - 7.24: 6303 7.24 - 9.66: 1046 9.66 - 12.07: 36 Bond angle restraints: 131856 Sorted by residual: angle pdb=" C ASP L 131 " pdb=" N PRO L 132 " pdb=" CA PRO L 132 " ideal model delta sigma weight residual 119.56 127.72 -8.16 1.02e+00 9.61e-01 6.40e+01 angle pdb=" C ASP 3 131 " pdb=" N PRO 3 132 " pdb=" CA PRO 3 132 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.36e+01 angle pdb=" C ASP 6 131 " pdb=" N PRO 6 132 " pdb=" CA PRO 6 132 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C ASP 0 131 " pdb=" N PRO 0 132 " pdb=" CA PRO 0 132 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C ASP O 131 " pdb=" N PRO O 132 " pdb=" CA PRO O 132 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 ... (remaining 131851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 31732 16.52 - 33.05: 1093 33.05 - 49.57: 458 49.57 - 66.09: 173 66.09 - 82.62: 36 Dihedral angle restraints: 33492 sinusoidal: 18996 harmonic: 14496 Sorted by residual: dihedral pdb=" CD2 HIS I 105 " pdb=" CG HIS I 105 " pdb=" ND1 HIS I 105 " pdb=" HD1 HIS I 105 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CD2 HIS 3 105 " pdb=" CG HIS 3 105 " pdb=" ND1 HIS 3 105 " pdb=" HD1 HIS 3 105 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CD2 HIS F 105 " pdb=" CG HIS F 105 " pdb=" ND1 HIS F 105 " pdb=" HD1 HIS F 105 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 33489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3463 0.110 - 0.219: 1792 0.219 - 0.329: 436 0.329 - 0.438: 69 0.438 - 0.548: 36 Chirality restraints: 5796 Sorted by residual: chirality pdb=" CG LEU 3 87 " pdb=" CB LEU 3 87 " pdb=" CD1 LEU 3 87 " pdb=" CD2 LEU 3 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" CG LEU O 87 " pdb=" CB LEU O 87 " pdb=" CD1 LEU O 87 " pdb=" CD2 LEU O 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 5793 not shown) Planarity restraints: 10956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS 3 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.26e+02 pdb=" CG HIS 3 105 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS 3 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS 3 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS 3 105 " 0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS 3 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS 3 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS 3 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS 3 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 105 " 0.076 2.00e-02 2.50e+03 7.49e-02 1.26e+02 pdb=" CG HIS I 105 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS I 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS I 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS I 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS I 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS I 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS I 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS I 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 105 " -0.076 2.00e-02 2.50e+03 7.49e-02 1.26e+02 pdb=" CG HIS F 105 " -0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS F 105 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS F 105 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS F 105 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS F 105 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 HIS F 105 " 0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS F 105 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 HIS F 105 " -0.057 2.00e-02 2.50e+03 ... (remaining 10953 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 1612 2.00 - 2.65: 98918 2.65 - 3.30: 210409 3.30 - 3.95: 283317 3.95 - 4.60: 440232 Nonbonded interactions: 1034488 Sorted by model distance: nonbonded pdb=" H SER X 134 " pdb=" H ASP X 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER F 134 " pdb=" H ASP F 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER B 134 " pdb=" H ASP B 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER 3 134 " pdb=" H ASP 3 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER R 134 " pdb=" H ASP R 135 " model vdw 1.354 2.100 ... (remaining 1034483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '7' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '8' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.950 Extract box with map and model: 1.920 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 114.110 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3038 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 : 0.031 0.202 35808 Z= 2.053 Angle : 1.769 11.026 48336 Z= 1.184 Chirality : 0.132 0.548 5796 Planarity : 0.010 0.075 6312 Dihedral : 9.860 82.618 13308 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.12), residues: 4752 helix: -0.93 (0.15), residues: 924 sheet: 1.04 (0.14), residues: 1464 loop : 0.92 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP T 48 HIS 0.005 0.002 HIS 0 105 PHE 0.019 0.007 PHE X 198 TYR 0.058 0.009 TYR B 257 ARG 0.015 0.002 ARG U 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 742 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 742 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5375 (mtm) cc_final: 0.4995 (mtp) REVERT: A 154 ASP cc_start: 0.5951 (t0) cc_final: 0.5514 (t0) REVERT: A 280 MET cc_start: 0.5767 (mmm) cc_final: 0.5422 (mmm) REVERT: B 23 MET cc_start: 0.3968 (mtp) cc_final: 0.3688 (mtm) REVERT: B 105 HIS cc_start: 0.4310 (p-80) cc_final: 0.2657 (m-70) REVERT: B 131 ASP cc_start: 0.4565 (t0) cc_final: 0.4275 (t0) REVERT: E 52 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6759 (mptt) REVERT: F 268 MET cc_start: 0.4668 (mmm) cc_final: 0.4467 (mmp) REVERT: F 280 MET cc_start: 0.4931 (mmm) cc_final: 0.4725 (mmt) REVERT: L 85 MET cc_start: 0.5237 (mtm) cc_final: 0.4768 (ttt) REVERT: L 154 ASP cc_start: 0.5936 (t0) cc_final: 0.5508 (t0) REVERT: L 220 GLU cc_start: 0.5094 (mt-10) cc_final: 0.4825 (mt-10) REVERT: L 280 MET cc_start: 0.6079 (mmm) cc_final: 0.5605 (mmm) REVERT: L 285 GLN cc_start: 0.4568 (mp10) cc_final: 0.4320 (mp10) REVERT: O 23 MET cc_start: 0.4574 (mtp) cc_final: 0.4348 (mtm) REVERT: O 85 MET cc_start: 0.4358 (mtm) cc_final: 0.4014 (ttt) REVERT: O 163 TYR cc_start: 0.4346 (m-80) cc_final: 0.3937 (m-80) REVERT: R 23 MET cc_start: 0.4935 (mtp) cc_final: 0.4690 (mtm) REVERT: R 85 MET cc_start: 0.4674 (mtm) cc_final: 0.4350 (ttt) REVERT: R 207 ARG cc_start: 0.4846 (mtt-85) cc_final: 0.4567 (mtt180) REVERT: U 105 HIS cc_start: 0.3139 (p-80) cc_final: 0.2039 (m90) REVERT: U 123 PHE cc_start: 0.5149 (m-80) cc_final: 0.4636 (m-80) REVERT: X 85 MET cc_start: 0.5132 (mtm) cc_final: 0.4920 (ttm) REVERT: X 114 LYS cc_start: 0.5592 (mmtt) cc_final: 0.5360 (mtmt) REVERT: X 124 ASP cc_start: 0.7315 (m-30) cc_final: 0.6892 (m-30) REVERT: X 154 ASP cc_start: 0.5662 (t0) cc_final: 0.5246 (t0) REVERT: X 216 ASN cc_start: 0.5487 (p0) cc_final: 0.5252 (p0) REVERT: X 220 GLU cc_start: 0.5127 (mt-10) cc_final: 0.4633 (mt-10) REVERT: 3 19 LEU cc_start: 0.5366 (mt) cc_final: 0.5133 (mp) REVERT: 3 85 MET cc_start: 0.5121 (mtm) cc_final: 0.4712 (ttt) REVERT: 3 99 TYR cc_start: 0.3508 (m-80) cc_final: 0.2982 (m-80) REVERT: 3 114 LYS cc_start: 0.6025 (mmtt) cc_final: 0.5822 (mtmt) REVERT: 3 353 GLU cc_start: 0.6844 (tt0) cc_final: 0.6450 (mp0) REVERT: 5 52 LYS cc_start: 0.5106 (mtpt) cc_final: 0.4627 (mptt) REVERT: 6 194 ASN cc_start: 0.3827 (m-40) cc_final: 0.3613 (m110) REVERT: 6 200 GLN cc_start: 0.3853 (tt0) cc_final: 0.3652 (tt0) REVERT: 8 52 LYS cc_start: 0.6617 (mtpt) cc_final: 0.6203 (mptt) outliers start: 0 outliers final: 0 residues processed: 742 average time/residue: 0.9943 time to fit residues: 1151.2553 Evaluate side-chains 506 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 5.9990 chunk 354 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 366 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 chunk 424 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 33 HIS B 314 ASN N 33 HIS O 314 ASN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 314 ASN Z 33 HIS 0 235 ASN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 314 ASN 6 355 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3271 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35808 Z= 0.379 Angle : 0.718 6.018 48336 Z= 0.406 Chirality : 0.053 0.210 5796 Planarity : 0.005 0.086 6312 Dihedral : 7.069 84.755 5040 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.03 % Rotamer: Outliers : 1.04 % Allowed : 5.04 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 4752 helix: 0.46 (0.17), residues: 912 sheet: 0.09 (0.13), residues: 1536 loop : 0.37 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 48 HIS 0.009 0.003 HIS W 33 PHE 0.029 0.003 PHE R 198 TYR 0.020 0.002 TYR 0 163 ARG 0.005 0.001 ARG X 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 581 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 542 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5841 (mtm) cc_final: 0.5386 (mtp) REVERT: A 133 ARG cc_start: 0.5440 (mmm-85) cc_final: 0.4939 (mmm160) REVERT: B 105 HIS cc_start: 0.4438 (p-80) cc_final: 0.4237 (p-80) REVERT: B 131 ASP cc_start: 0.4338 (t0) cc_final: 0.3886 (t0) REVERT: B 232 ASP cc_start: 0.6822 (m-30) cc_final: 0.6363 (t0) REVERT: E 52 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6739 (mptt) REVERT: F 85 MET cc_start: 0.4854 (mtm) cc_final: 0.4471 (mtp) REVERT: I 133 ARG cc_start: 0.5977 (mmm-85) cc_final: 0.5648 (mmm-85) REVERT: L 85 MET cc_start: 0.5180 (mtm) cc_final: 0.4689 (ttt) REVERT: L 280 MET cc_start: 0.5899 (mmm) cc_final: 0.5542 (mmm) REVERT: L 285 GLN cc_start: 0.4507 (mp10) cc_final: 0.4148 (mp10) REVERT: L 305 LYS cc_start: 0.4945 (mmtp) cc_final: 0.4488 (mmmt) REVERT: O 124 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: O 286 ARG cc_start: 0.3788 (mtt-85) cc_final: 0.3537 (mtm110) REVERT: R 23 MET cc_start: 0.5132 (mtp) cc_final: 0.4784 (mtp) REVERT: R 85 MET cc_start: 0.4547 (mtm) cc_final: 0.4287 (ttt) REVERT: R 207 ARG cc_start: 0.5021 (mtt-85) cc_final: 0.4809 (mtt180) REVERT: U 105 HIS cc_start: 0.3169 (p-80) cc_final: 0.2015 (m170) REVERT: U 123 PHE cc_start: 0.5339 (m-80) cc_final: 0.5117 (m-80) REVERT: X 85 MET cc_start: 0.4857 (mtm) cc_final: 0.4639 (ttm) REVERT: X 232 ASP cc_start: 0.7613 (m-30) cc_final: 0.7401 (t0) REVERT: 0 226 THR cc_start: 0.7611 (m) cc_final: 0.7409 (m) REVERT: 0 242 ILE cc_start: 0.5891 (mt) cc_final: 0.5674 (pt) REVERT: 3 32 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6299 (mp0) REVERT: 3 105 HIS cc_start: 0.4243 (p-80) cc_final: 0.3069 (m90) REVERT: 3 316 LYS cc_start: 0.4368 (pttt) cc_final: 0.4145 (mmtt) REVERT: 3 353 GLU cc_start: 0.6617 (tt0) cc_final: 0.6180 (mp0) REVERT: 5 52 LYS cc_start: 0.6137 (mtpt) cc_final: 0.5656 (mptt) REVERT: 8 52 LYS cc_start: 0.6807 (mtpt) cc_final: 0.6322 (mptt) outliers start: 39 outliers final: 26 residues processed: 566 average time/residue: 1.0059 time to fit residues: 895.1583 Evaluate side-chains 504 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 477 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain a residue 33 HIS Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain N residue 33 HIS Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 314 ASN Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 108 ASP Chi-restraints excluded: chain Z residue 30 ILE Chi-restraints excluded: chain 0 residue 101 VAL Chi-restraints excluded: chain 0 residue 285 GLN Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 2 residue 33 HIS Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 4 residue 386 VAL Chi-restraints excluded: chain 6 residue 314 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 425 optimal weight: 7.9990 chunk 459 optimal weight: 20.0000 chunk 379 optimal weight: 9.9990 chunk 422 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 314 ASN F 206 ASN G 412 GLN I 314 ASN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 314 ASN ** X 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 103 ASN 6 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3312 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35808 Z= 0.252 Angle : 0.567 9.018 48336 Z= 0.322 Chirality : 0.048 0.176 5796 Planarity : 0.004 0.075 6312 Dihedral : 6.652 83.161 5040 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.09 % Allowed : 6.50 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.12), residues: 4752 helix: 1.14 (0.19), residues: 912 sheet: 0.33 (0.14), residues: 1404 loop : -0.07 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 48 HIS 0.021 0.003 HIS a 33 PHE 0.017 0.002 PHE 0 198 TYR 0.012 0.001 TYR 1 444 ARG 0.006 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 540 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 499 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5682 (mtm) cc_final: 0.5261 (mtp) REVERT: B 232 ASP cc_start: 0.6980 (m-30) cc_final: 0.6508 (t0) REVERT: F 85 MET cc_start: 0.4698 (mtm) cc_final: 0.4336 (mtp) REVERT: F 280 MET cc_start: 0.5367 (tpt) cc_final: 0.5051 (mmt) REVERT: I 133 ARG cc_start: 0.6194 (mmm-85) cc_final: 0.5913 (mmm-85) REVERT: I 194 ASN cc_start: 0.4308 (m-40) cc_final: 0.3833 (m110) REVERT: L 85 MET cc_start: 0.5176 (mtm) cc_final: 0.4769 (ttt) REVERT: L 124 ASP cc_start: 0.7550 (m-30) cc_final: 0.7248 (m-30) REVERT: L 280 MET cc_start: 0.5877 (mmm) cc_final: 0.5577 (mmt) REVERT: L 285 GLN cc_start: 0.4491 (mp10) cc_final: 0.4275 (mp10) REVERT: L 305 LYS cc_start: 0.5233 (mmtp) cc_final: 0.4784 (mmmt) REVERT: O 18 MET cc_start: 0.5192 (tmm) cc_final: 0.4935 (tmm) REVERT: O 23 MET cc_start: 0.5318 (mtp) cc_final: 0.4975 (mtm) REVERT: O 124 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: R 23 MET cc_start: 0.5355 (mtp) cc_final: 0.5087 (mtm) REVERT: R 85 MET cc_start: 0.4625 (mtm) cc_final: 0.4266 (ttt) REVERT: R 175 GLU cc_start: 0.5287 (tt0) cc_final: 0.5067 (tt0) REVERT: R 207 ARG cc_start: 0.5008 (mtt-85) cc_final: 0.4794 (mtm-85) REVERT: S 447 MET cc_start: 0.5080 (mtp) cc_final: 0.4829 (ttp) REVERT: X 85 MET cc_start: 0.4934 (mtm) cc_final: 0.4702 (ttm) REVERT: X 232 ASP cc_start: 0.7481 (m-30) cc_final: 0.7222 (t0) REVERT: 2 31 LEU cc_start: 0.4819 (mm) cc_final: 0.4551 (mm) REVERT: 3 353 GLU cc_start: 0.6756 (tt0) cc_final: 0.6302 (mp0) REVERT: 5 52 LYS cc_start: 0.6223 (mtpt) cc_final: 0.5683 (mptt) outliers start: 41 outliers final: 28 residues processed: 525 average time/residue: 1.0495 time to fit residues: 854.4332 Evaluate side-chains 491 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 462 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain a residue 33 HIS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 314 ASN Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 444 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 138 LEU Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain 0 residue 271 GLU Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 1 residue 408 ILE Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 8.9990 chunk 320 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 452 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 404 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 GLN X 103 ASN X 105 HIS ** 0 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3400 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35808 Z= 0.377 Angle : 0.634 10.750 48336 Z= 0.356 Chirality : 0.052 0.183 5796 Planarity : 0.005 0.060 6312 Dihedral : 6.679 82.209 5040 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.35 % Allowed : 8.49 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4752 helix: 0.90 (0.18), residues: 900 sheet: 0.00 (0.14), residues: 1344 loop : -0.69 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 48 HIS 0.017 0.003 HIS R 105 PHE 0.029 0.003 PHE I 198 TYR 0.014 0.002 TYR 2 34 ARG 0.007 0.001 ARG L 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 479 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5710 (mtm) cc_final: 0.5303 (mtp) REVERT: A 133 ARG cc_start: 0.5575 (mmm-85) cc_final: 0.5236 (mmm160) REVERT: A 318 ILE cc_start: 0.7397 (mm) cc_final: 0.7162 (mm) REVERT: B 23 MET cc_start: 0.5780 (mtp) cc_final: 0.5487 (mtm) REVERT: F 85 MET cc_start: 0.4799 (mtm) cc_final: 0.4463 (mtp) REVERT: F 280 MET cc_start: 0.5549 (tpt) cc_final: 0.5188 (mmt) REVERT: I 133 ARG cc_start: 0.6232 (mmm-85) cc_final: 0.5961 (mmm-85) REVERT: L 85 MET cc_start: 0.5235 (mtm) cc_final: 0.4802 (mtp) REVERT: L 131 ASP cc_start: 0.3976 (t0) cc_final: 0.3537 (t0) REVERT: L 280 MET cc_start: 0.5837 (mmm) cc_final: 0.5392 (mmm) REVERT: L 285 GLN cc_start: 0.4313 (mp10) cc_final: 0.4066 (mp10) REVERT: L 305 LYS cc_start: 0.5669 (mmtp) cc_final: 0.5224 (mmmt) REVERT: M 444 TYR cc_start: 0.4497 (m-80) cc_final: 0.4171 (m-80) REVERT: O 23 MET cc_start: 0.5759 (mtp) cc_final: 0.5367 (mtm) REVERT: O 124 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: O 286 ARG cc_start: 0.4465 (mtt-85) cc_final: 0.4099 (mtm110) REVERT: R 85 MET cc_start: 0.4942 (mtm) cc_final: 0.4591 (mtp) REVERT: S 447 MET cc_start: 0.5233 (mtp) cc_final: 0.4979 (ttp) REVERT: V 444 TYR cc_start: 0.4136 (m-80) cc_final: 0.3870 (m-80) REVERT: X 85 MET cc_start: 0.4978 (mtm) cc_final: 0.4718 (ttm) REVERT: X 280 MET cc_start: 0.5915 (mmm) cc_final: 0.5464 (mmm) REVERT: Y 444 TYR cc_start: 0.4406 (m-80) cc_final: 0.4159 (m-80) REVERT: 5 52 LYS cc_start: 0.6614 (mtpt) cc_final: 0.6057 (mptt) REVERT: 6 23 MET cc_start: 0.5825 (mtp) cc_final: 0.5300 (mtp) outliers start: 51 outliers final: 38 residues processed: 512 average time/residue: 1.0306 time to fit residues: 818.5632 Evaluate side-chains 468 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 429 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 127 MET Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain 0 residue 101 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 1 residue 408 ILE Chi-restraints excluded: chain 3 residue 103 ASN Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 6 residue 12 MET Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 162 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 312 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 406 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 GLN F 209 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 ASN ** O 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN ** U 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 437 GLN ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 GLN 6 200 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3439 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 35808 Z= 0.370 Angle : 0.618 9.154 48336 Z= 0.345 Chirality : 0.051 0.179 5796 Planarity : 0.005 0.075 6312 Dihedral : 6.590 82.451 5040 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.02 % Allowed : 9.47 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4752 helix: 0.49 (0.17), residues: 912 sheet: -0.21 (0.14), residues: 1296 loop : -1.16 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP W 48 HIS 0.018 0.003 HIS B 105 PHE 0.022 0.003 PHE I 198 TYR 0.013 0.002 TYR 2 34 ARG 0.010 0.001 ARG X 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 521 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 445 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5621 (mtm) cc_final: 0.5190 (mtp) REVERT: A 318 ILE cc_start: 0.7436 (mm) cc_final: 0.7202 (mm) REVERT: F 85 MET cc_start: 0.4828 (mtm) cc_final: 0.4503 (mtp) REVERT: I 133 ARG cc_start: 0.6062 (mmm-85) cc_final: 0.5759 (mmm-85) REVERT: L 85 MET cc_start: 0.5273 (mtm) cc_final: 0.4879 (mtp) REVERT: L 280 MET cc_start: 0.5836 (mmm) cc_final: 0.5401 (mmm) REVERT: L 285 GLN cc_start: 0.4355 (mp10) cc_final: 0.4135 (mp10) REVERT: L 305 LYS cc_start: 0.5593 (mmtp) cc_final: 0.5101 (mmmt) REVERT: M 444 TYR cc_start: 0.4488 (m-80) cc_final: 0.4134 (m-80) REVERT: O 124 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: R 85 MET cc_start: 0.5129 (mtm) cc_final: 0.4681 (mtp) REVERT: S 447 MET cc_start: 0.5175 (mtp) cc_final: 0.4965 (ttp) REVERT: X 85 MET cc_start: 0.4991 (mtm) cc_final: 0.4714 (mtp) REVERT: X 138 LEU cc_start: 0.3888 (OUTLIER) cc_final: 0.3566 (tt) REVERT: X 280 MET cc_start: 0.5596 (mmm) cc_final: 0.5119 (mmm) REVERT: Y 444 TYR cc_start: 0.4465 (m-80) cc_final: 0.4213 (m-80) REVERT: 0 23 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.5226 (mtp) REVERT: 5 52 LYS cc_start: 0.6815 (mtpt) cc_final: 0.6180 (mptt) REVERT: 6 156 ASP cc_start: 0.6394 (p0) cc_final: 0.6117 (p0) REVERT: 6 193 GLU cc_start: 0.5241 (pm20) cc_final: 0.4994 (pm20) outliers start: 76 outliers final: 51 residues processed: 499 average time/residue: 1.0367 time to fit residues: 806.1764 Evaluate side-chains 471 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 417 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 408 ILE Chi-restraints excluded: chain P residue 447 MET Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 268 MET Chi-restraints excluded: chain V residue 437 GLN Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain 0 residue 23 MET Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 1 residue 408 ILE Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 215 VAL Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 5 residue 30 ILE Chi-restraints excluded: chain 6 residue 12 MET Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 127 MET Chi-restraints excluded: chain 6 residue 162 ASP Chi-restraints excluded: chain 6 residue 215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 0.9980 chunk 407 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 265 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 452 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3423 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35808 Z= 0.199 Angle : 0.507 4.554 48336 Z= 0.282 Chirality : 0.047 0.165 5796 Planarity : 0.004 0.069 6312 Dihedral : 6.220 81.658 5040 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.46 % Allowed : 10.19 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4752 helix: 0.97 (0.18), residues: 900 sheet: -0.08 (0.14), residues: 1296 loop : -0.98 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 48 HIS 0.007 0.002 HIS B 105 PHE 0.013 0.002 PHE I 198 TYR 0.010 0.001 TYR I 99 ARG 0.007 0.000 ARG O 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 492 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 437 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5645 (mtm) cc_final: 0.5223 (mtp) REVERT: A 318 ILE cc_start: 0.7395 (mm) cc_final: 0.7144 (mm) REVERT: F 85 MET cc_start: 0.4905 (mtm) cc_final: 0.4614 (mtp) REVERT: I 133 ARG cc_start: 0.5996 (mmm-85) cc_final: 0.5717 (mmm-85) REVERT: I 193 GLU cc_start: 0.5049 (pm20) cc_final: 0.4812 (pm20) REVERT: L 85 MET cc_start: 0.5075 (mtm) cc_final: 0.4714 (mtp) REVERT: L 280 MET cc_start: 0.5920 (mmm) cc_final: 0.5493 (mmm) REVERT: L 305 LYS cc_start: 0.5589 (mmtp) cc_final: 0.5111 (mmmt) REVERT: M 444 TYR cc_start: 0.4409 (m-80) cc_final: 0.4069 (m-80) REVERT: O 23 MET cc_start: 0.5904 (mtp) cc_final: 0.5630 (mtm) REVERT: O 124 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: R 85 MET cc_start: 0.4993 (mtm) cc_final: 0.4515 (mtp) REVERT: S 447 MET cc_start: 0.5186 (mtp) cc_final: 0.4971 (ttp) REVERT: U 133 ARG cc_start: 0.5449 (mmm-85) cc_final: 0.5148 (mmm-85) REVERT: U 154 ASP cc_start: 0.6881 (p0) cc_final: 0.6555 (p0) REVERT: X 85 MET cc_start: 0.5020 (mtm) cc_final: 0.4697 (mtp) REVERT: X 131 ASP cc_start: 0.4273 (t0) cc_final: 0.3852 (t0) REVERT: X 138 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3413 (tt) REVERT: X 280 MET cc_start: 0.5650 (mmm) cc_final: 0.5181 (mmm) REVERT: Y 444 TYR cc_start: 0.4427 (m-80) cc_final: 0.4190 (m-80) REVERT: 5 52 LYS cc_start: 0.6633 (mtpt) cc_final: 0.6054 (mptt) REVERT: 6 154 ASP cc_start: 0.6630 (p0) cc_final: 0.6169 (p0) REVERT: 6 156 ASP cc_start: 0.6281 (p0) cc_final: 0.5792 (p0) REVERT: 6 193 GLU cc_start: 0.5135 (pm20) cc_final: 0.4894 (pm20) outliers start: 55 outliers final: 43 residues processed: 478 average time/residue: 1.0045 time to fit residues: 745.2438 Evaluate side-chains 471 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 426 time to evaluate : 4.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain P residue 447 MET Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 127 MET Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 215 VAL Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 179 SER Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 3 residue 352 LEU Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 12 MET Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 162 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 330 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 381 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 451 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 200 GLN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 GLN ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3456 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35808 Z= 0.334 Angle : 0.577 9.246 48336 Z= 0.322 Chirality : 0.050 0.164 5796 Planarity : 0.004 0.071 6312 Dihedral : 6.302 82.622 5040 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.12 % Allowed : 10.83 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4752 helix: 0.73 (0.17), residues: 900 sheet: -0.31 (0.14), residues: 1296 loop : -1.26 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 48 HIS 0.009 0.002 HIS B 105 PHE 0.020 0.003 PHE I 198 TYR 0.010 0.002 TYR I 257 ARG 0.007 0.001 ARG X 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 443 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5680 (mtm) cc_final: 0.5263 (mtp) REVERT: A 152 MET cc_start: 0.4796 (mtt) cc_final: 0.4470 (mtt) REVERT: A 318 ILE cc_start: 0.7341 (mm) cc_final: 0.7115 (mm) REVERT: F 85 MET cc_start: 0.4796 (mtm) cc_final: 0.4498 (mtp) REVERT: L 85 MET cc_start: 0.5162 (mtm) cc_final: 0.4744 (mtp) REVERT: L 280 MET cc_start: 0.5895 (mmm) cc_final: 0.5480 (mmm) REVERT: L 305 LYS cc_start: 0.5664 (mmtp) cc_final: 0.5160 (mmmt) REVERT: M 444 TYR cc_start: 0.4419 (m-80) cc_final: 0.4113 (m-80) REVERT: O 229 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4066 (tt) REVERT: R 85 MET cc_start: 0.5267 (mtm) cc_final: 0.4758 (mtp) REVERT: S 447 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4707 (ttp) REVERT: U 154 ASP cc_start: 0.6834 (p0) cc_final: 0.6457 (p0) REVERT: X 85 MET cc_start: 0.5046 (mtm) cc_final: 0.4713 (mtp) REVERT: X 138 LEU cc_start: 0.3871 (OUTLIER) cc_final: 0.3551 (tt) REVERT: X 280 MET cc_start: 0.5630 (mmm) cc_final: 0.5155 (mmm) REVERT: Y 444 TYR cc_start: 0.4424 (m-80) cc_final: 0.4168 (m-80) REVERT: 0 250 LEU cc_start: 0.4614 (mt) cc_final: 0.4377 (tt) REVERT: 5 52 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6131 (mptt) REVERT: 6 154 ASP cc_start: 0.6669 (p0) cc_final: 0.6282 (p0) REVERT: 6 193 GLU cc_start: 0.5244 (pm20) cc_final: 0.5042 (pm20) outliers start: 80 outliers final: 69 residues processed: 498 average time/residue: 1.0403 time to fit residues: 809.3588 Evaluate side-chains 501 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 429 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain O residue 229 LEU Chi-restraints excluded: chain P residue 447 MET Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 268 MET Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 152 MET Chi-restraints excluded: chain X residue 215 VAL Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 102 THR Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 103 ASN Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 179 SER Chi-restraints excluded: chain 3 residue 215 VAL Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 3 residue 352 LEU Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 12 MET Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain 6 residue 102 THR Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 127 MET Chi-restraints excluded: chain 6 residue 162 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 135 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 223 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3431 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 35808 Z= 0.164 Angle : 0.484 4.840 48336 Z= 0.267 Chirality : 0.046 0.162 5796 Planarity : 0.004 0.070 6312 Dihedral : 5.973 81.781 5040 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.46 % Allowed : 11.78 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4752 helix: 1.15 (0.18), residues: 900 sheet: -0.13 (0.14), residues: 1296 loop : -1.01 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 48 HIS 0.005 0.001 HIS B 105 PHE 0.012 0.001 PHE W 36 TYR 0.013 0.001 TYR L 257 ARG 0.008 0.000 ARG I 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 432 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5624 (mtm) cc_final: 0.5231 (mtp) REVERT: A 318 ILE cc_start: 0.7380 (mm) cc_final: 0.7163 (mm) REVERT: F 85 MET cc_start: 0.4842 (mtm) cc_final: 0.4559 (mtp) REVERT: I 133 ARG cc_start: 0.5939 (mmm-85) cc_final: 0.5542 (mmm-85) REVERT: L 85 MET cc_start: 0.5012 (mtm) cc_final: 0.4614 (mtp) REVERT: L 280 MET cc_start: 0.5890 (mmm) cc_final: 0.5468 (mmm) REVERT: L 305 LYS cc_start: 0.5659 (mmtp) cc_final: 0.5155 (mmmt) REVERT: M 444 TYR cc_start: 0.4420 (m-80) cc_final: 0.4116 (m-80) REVERT: R 85 MET cc_start: 0.5157 (mtm) cc_final: 0.4651 (mtp) REVERT: S 447 MET cc_start: 0.5080 (OUTLIER) cc_final: 0.4860 (ttp) REVERT: U 133 ARG cc_start: 0.5298 (mmm-85) cc_final: 0.4990 (mmm-85) REVERT: U 154 ASP cc_start: 0.6758 (p0) cc_final: 0.6394 (p0) REVERT: X 85 MET cc_start: 0.4969 (mtm) cc_final: 0.4657 (mtp) REVERT: X 138 LEU cc_start: 0.3850 (OUTLIER) cc_final: 0.3502 (tt) REVERT: X 280 MET cc_start: 0.5665 (mmm) cc_final: 0.5067 (mmm) REVERT: Y 444 TYR cc_start: 0.4388 (m-80) cc_final: 0.4137 (m-80) REVERT: 5 52 LYS cc_start: 0.6656 (mtpt) cc_final: 0.6074 (mptt) REVERT: 6 156 ASP cc_start: 0.6484 (p0) cc_final: 0.6228 (p0) outliers start: 55 outliers final: 44 residues processed: 470 average time/residue: 1.0177 time to fit residues: 745.2132 Evaluate side-chains 456 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 410 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 127 MET Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 152 MET Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 215 VAL Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 3 residue 352 LEU Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 5 residue 30 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 127 MET Chi-restraints excluded: chain 6 residue 215 VAL Chi-restraints excluded: chain 6 residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 chunk 394 optimal weight: 1.9990 chunk 420 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 379 optimal weight: 7.9990 chunk 397 optimal weight: 4.9990 chunk 418 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 259 GLN ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3459 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35808 Z= 0.287 Angle : 0.544 4.872 48336 Z= 0.302 Chirality : 0.049 0.161 5796 Planarity : 0.004 0.073 6312 Dihedral : 6.089 82.527 5040 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.62 % Allowed : 11.94 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4752 helix: 1.01 (0.17), residues: 900 sheet: -0.32 (0.14), residues: 1296 loop : -1.20 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 48 HIS 0.007 0.002 HIS B 105 PHE 0.016 0.002 PHE L 198 TYR 0.012 0.001 TYR 0 257 ARG 0.009 0.001 ARG L 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 483 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 422 time to evaluate : 4.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5627 (mtm) cc_final: 0.5217 (mtp) REVERT: A 152 MET cc_start: 0.4788 (mtt) cc_final: 0.4478 (mtt) REVERT: A 318 ILE cc_start: 0.7403 (mm) cc_final: 0.7191 (mm) REVERT: F 85 MET cc_start: 0.4926 (mtm) cc_final: 0.4640 (mtp) REVERT: F 280 MET cc_start: 0.5641 (tpt) cc_final: 0.5361 (mmt) REVERT: K 35 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6362 (mmtp) REVERT: L 85 MET cc_start: 0.5083 (mtm) cc_final: 0.4677 (mtp) REVERT: L 280 MET cc_start: 0.5936 (mmm) cc_final: 0.5513 (mmm) REVERT: L 305 LYS cc_start: 0.5767 (mmtp) cc_final: 0.5235 (mmmt) REVERT: M 444 TYR cc_start: 0.4400 (m-80) cc_final: 0.4107 (m-80) REVERT: O 280 MET cc_start: 0.5460 (mmt) cc_final: 0.5186 (mmm) REVERT: R 85 MET cc_start: 0.5174 (mtm) cc_final: 0.4731 (mtp) REVERT: S 447 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4704 (ttp) REVERT: U 133 ARG cc_start: 0.5124 (mmm-85) cc_final: 0.4785 (mmm-85) REVERT: U 154 ASP cc_start: 0.6798 (p0) cc_final: 0.6437 (p0) REVERT: X 85 MET cc_start: 0.5030 (mtm) cc_final: 0.4704 (mtp) REVERT: X 131 ASP cc_start: 0.4384 (t0) cc_final: 0.3927 (t0) REVERT: X 138 LEU cc_start: 0.3923 (OUTLIER) cc_final: 0.3599 (tt) REVERT: X 280 MET cc_start: 0.5675 (mmm) cc_final: 0.5074 (mmm) REVERT: Y 444 TYR cc_start: 0.4350 (m-80) cc_final: 0.4099 (m-80) REVERT: 1 448 GLN cc_start: 0.4386 (mm-40) cc_final: 0.4034 (mm-40) REVERT: 5 52 LYS cc_start: 0.6737 (mtpt) cc_final: 0.6123 (mptt) REVERT: 6 156 ASP cc_start: 0.6495 (p0) cc_final: 0.6244 (p0) outliers start: 61 outliers final: 54 residues processed: 465 average time/residue: 1.0111 time to fit residues: 730.6315 Evaluate side-chains 468 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 411 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 268 MET Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 152 MET Chi-restraints excluded: chain X residue 215 VAL Chi-restraints excluded: chain 0 residue 102 THR Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 179 SER Chi-restraints excluded: chain 3 residue 215 VAL Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 3 residue 352 LEU Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 127 MET Chi-restraints excluded: chain 6 residue 162 ASP Chi-restraints excluded: chain 6 residue 215 VAL Chi-restraints excluded: chain 6 residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 4.9990 chunk 444 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 466 optimal weight: 7.9990 chunk 429 optimal weight: 2.9990 chunk 371 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 286 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 225 ASN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3465 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35808 Z= 0.299 Angle : 0.547 5.925 48336 Z= 0.304 Chirality : 0.049 0.159 5796 Planarity : 0.004 0.091 6312 Dihedral : 6.140 84.349 5040 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.67 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4752 helix: 0.88 (0.17), residues: 912 sheet: -0.43 (0.14), residues: 1296 loop : -1.41 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 48 HIS 0.006 0.002 HIS B 105 PHE 0.017 0.002 PHE 3 198 TYR 0.020 0.001 TYR U 257 ARG 0.009 0.001 ARG B 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 421 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5644 (mtm) cc_final: 0.5227 (mtp) REVERT: A 152 MET cc_start: 0.4744 (mtt) cc_final: 0.4416 (mtt) REVERT: A 318 ILE cc_start: 0.7446 (mm) cc_final: 0.7229 (mm) REVERT: F 85 MET cc_start: 0.5042 (mtm) cc_final: 0.4733 (mtp) REVERT: F 280 MET cc_start: 0.5794 (tpt) cc_final: 0.5564 (mmt) REVERT: K 35 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6442 (mmtp) REVERT: L 85 MET cc_start: 0.4994 (mtm) cc_final: 0.4641 (mtp) REVERT: L 131 ASP cc_start: 0.3826 (t0) cc_final: 0.3535 (t0) REVERT: L 280 MET cc_start: 0.5953 (mmm) cc_final: 0.5549 (mmm) REVERT: L 305 LYS cc_start: 0.5814 (mmtp) cc_final: 0.5267 (mmmt) REVERT: M 444 TYR cc_start: 0.4219 (m-80) cc_final: 0.3958 (m-80) REVERT: R 85 MET cc_start: 0.5011 (mtm) cc_final: 0.4559 (mtp) REVERT: U 152 MET cc_start: 0.4382 (mtt) cc_final: 0.4144 (mtt) REVERT: U 154 ASP cc_start: 0.6782 (p0) cc_final: 0.6430 (p0) REVERT: X 85 MET cc_start: 0.5194 (mtm) cc_final: 0.4811 (mtp) REVERT: X 131 ASP cc_start: 0.4364 (t0) cc_final: 0.3927 (t0) REVERT: X 138 LEU cc_start: 0.3800 (OUTLIER) cc_final: 0.3471 (tt) REVERT: X 280 MET cc_start: 0.5644 (mmm) cc_final: 0.5026 (mmm) REVERT: Y 444 TYR cc_start: 0.4360 (m-80) cc_final: 0.4114 (m-80) REVERT: 1 448 GLN cc_start: 0.4535 (mm-40) cc_final: 0.4183 (mm-40) REVERT: 5 52 LYS cc_start: 0.6804 (mtpt) cc_final: 0.6179 (mptt) outliers start: 63 outliers final: 57 residues processed: 465 average time/residue: 1.0440 time to fit residues: 757.3175 Evaluate side-chains 463 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 404 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 268 MET Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 200 GLN Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain M residue 437 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 215 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain U residue 268 MET Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 102 THR Chi-restraints excluded: chain X residue 124 ASP Chi-restraints excluded: chain X residue 138 LEU Chi-restraints excluded: chain X residue 152 MET Chi-restraints excluded: chain X residue 215 VAL Chi-restraints excluded: chain 0 residue 102 THR Chi-restraints excluded: chain 0 residue 115 VAL Chi-restraints excluded: chain 0 residue 182 VAL Chi-restraints excluded: chain 0 residue 215 VAL Chi-restraints excluded: chain 0 residue 298 SER Chi-restraints excluded: chain 3 residue 102 THR Chi-restraints excluded: chain 3 residue 165 VAL Chi-restraints excluded: chain 3 residue 179 SER Chi-restraints excluded: chain 3 residue 215 VAL Chi-restraints excluded: chain 3 residue 273 ASN Chi-restraints excluded: chain 3 residue 351 ASN Chi-restraints excluded: chain 3 residue 352 LEU Chi-restraints excluded: chain 4 residue 437 GLN Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 127 MET Chi-restraints excluded: chain 6 residue 162 ASP Chi-restraints excluded: chain 6 residue 215 VAL Chi-restraints excluded: chain 6 residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 9.9990 chunk 395 optimal weight: 0.0060 chunk 113 optimal weight: 0.0170 chunk 342 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 371 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.269072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.200225 restraints weight = 108240.047| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.59 r_work: 0.3970 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35808 Z= 0.189 Angle : 0.498 6.780 48336 Z= 0.275 Chirality : 0.047 0.161 5796 Planarity : 0.004 0.071 6312 Dihedral : 5.916 84.533 5040 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.43 % Allowed : 12.63 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4752 helix: 1.16 (0.18), residues: 912 sheet: -0.32 (0.14), residues: 1296 loop : -1.25 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 48 HIS 0.004 0.001 HIS B 105 PHE 0.014 0.002 PHE 8 36 TYR 0.013 0.001 TYR U 257 ARG 0.008 0.001 ARG G 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16443.07 seconds wall clock time: 279 minutes 57.62 seconds (16797.62 seconds total)