Starting phenix.real_space_refine on Mon Aug 25 11:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp7_60328/08_2025/8zp7_60328.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.667 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 573 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 91 5.49 5 Mg 2 5.21 5 S 113 5.16 5 C 17131 2.51 5 N 4839 2.21 5 O 5364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27540 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1258 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 10, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 26, 'rna3p': 32} Chain breaks: 1 Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3495 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 413} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1352 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 156} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2819 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2878 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 13, 'TRANS': 361} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2854 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 359} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2845 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 360} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2701 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1927 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2701 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 317} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2039 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2398 SG CYS C 218 51.401 32.473 32.677 1.00102.41 S ATOM 24206 SG CYS B 298 73.205 43.894 123.509 1.00 92.92 S ATOM 24227 SG CYS B 301 74.199 46.411 125.921 1.00106.87 S ATOM 24468 SG CYS B 332 72.436 48.319 123.198 1.00108.29 S Time building chain proxies: 6.10, per 1000 atoms: 0.22 Number of scatterers: 27540 At special positions: 0 Unit cell: (112.312, 129.28, 191.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 91 15.00 Mg 2 11.99 O 5364 8.00 N 4839 7.00 C 17131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 762.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6166 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 34 sheets defined 37.4% alpha, 17.1% beta 14 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 155 through 162 removed outlier: 3.815A pdb=" N TRP C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.779A pdb=" N LEU C 375 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE C 376 " --> pdb=" O SER C 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 376' Processing helix chain 'C' and resid 418 through 426 Processing helix chain 'C' and resid 427 through 438 removed outlier: 4.468A pdb=" N ALA C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'C' and resid 456 through 465 Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.786A pdb=" N SER C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 514 Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 34 through 52 removed outlier: 3.705A pdb=" N PHE E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Proline residue: E 47 - end of helix Processing helix chain 'E' and resid 57 through 72 Processing helix chain 'E' and resid 80 through 88 removed outlier: 4.536A pdb=" N GLY E 86 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 108 through 111 removed outlier: 3.990A pdb=" N LEU E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.517A pdb=" N HIS E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 149 through 166 removed outlier: 4.204A pdb=" N LYS E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 166 " --> pdb=" O LYS E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 49 through 53 removed outlier: 4.116A pdb=" N LYS F 53 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.546A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 89 Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.682A pdb=" N ASP F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 233 through 251 removed outlier: 3.523A pdb=" N ALA F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 285 removed outlier: 4.198A pdb=" N ASN F 282 " --> pdb=" O SER F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.505A pdb=" N ILE H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 77 through 89 Processing helix chain 'H' and resid 107 through 117 Processing helix chain 'H' and resid 122 through 136 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 295 through 316 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 362 removed outlier: 3.608A pdb=" N GLY H 362 " --> pdb=" O LEU H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 52 through 56 Processing helix chain 'I' and resid 63 through 70 removed outlier: 3.501A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 89 Processing helix chain 'I' and resid 105 through 116 removed outlier: 3.523A pdb=" N ARG I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE I 114 " --> pdb=" O ASP I 110 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 135 Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 233 through 251 removed outlier: 3.603A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 286 removed outlier: 3.523A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 316 removed outlier: 3.712A pdb=" N TYR I 316 " --> pdb=" O ARG I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 361 Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.618A pdb=" N VAL I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN I 370 " --> pdb=" O TRP I 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 365 through 370' Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.648A pdb=" N LYS J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA J 54 " --> pdb=" O ASP J 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 50 through 54' Processing helix chain 'J' and resid 63 through 73 removed outlier: 3.776A pdb=" N GLY J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 Processing helix chain 'J' and resid 107 through 117 removed outlier: 3.671A pdb=" N LEU J 111 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 removed outlier: 3.628A pdb=" N VAL J 132 " --> pdb=" O GLN J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 145 Processing helix chain 'J' and resid 223 through 230 Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 279 through 285 removed outlier: 4.467A pdb=" N ASN J 282 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 285 " --> pdb=" O ASN J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 315 Processing helix chain 'J' and resid 349 through 362 Processing helix chain 'J' and resid 367 through 372 removed outlier: 3.751A pdb=" N LYS J 371 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER J 372 " --> pdb=" O VAL J 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 4.091A pdb=" N LEU K 16 " --> pdb=" O PRO K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 48 Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.687A pdb=" N LEU K 56 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 removed outlier: 3.999A pdb=" N LEU K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 89 Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'K' and resid 121 through 133 Processing helix chain 'K' and resid 139 through 146 Processing helix chain 'K' and resid 223 through 230 Processing helix chain 'K' and resid 234 through 250 Processing helix chain 'K' and resid 280 through 285 Processing helix chain 'K' and resid 292 through 294 No H-bonds generated for 'chain 'K' and resid 292 through 294' Processing helix chain 'K' and resid 295 through 315 removed outlier: 3.537A pdb=" N GLN K 299 " --> pdb=" O ASP K 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR K 315 " --> pdb=" O ILE K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 329 through 332 Processing helix chain 'K' and resid 349 through 359 Processing helix chain 'K' and resid 365 through 369 Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 223 through 229 Processing helix chain 'G' and resid 233 through 251 Processing helix chain 'G' and resid 279 through 286 removed outlier: 4.403A pdb=" N ASN G 282 " --> pdb=" O SER G 279 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG G 286 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 310 removed outlier: 3.697A pdb=" N ASP G 310 " --> pdb=" O ASN G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 349 through 362 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.969A pdb=" N ALA B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.692A pdb=" N LEU B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.757A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.796A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.582A pdb=" N ASP B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 341 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.536A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 370 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.813A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 removed outlier: 4.070A pdb=" N VAL D 31 " --> pdb=" O ASN D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.768A pdb=" N ARG D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 183 removed outlier: 3.610A pdb=" N ALA D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.504A pdb=" N PHE D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA2, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 248 through 252 removed outlier: 3.827A pdb=" N LYS C 389 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 404 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP C 398 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 74 through 75 removed outlier: 5.624A pdb=" N GLU E 74 " --> pdb=" O LEU E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.687A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.687A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'F' and resid 185 through 191 removed outlier: 3.581A pdb=" N HIS F 204 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 28 removed outlier: 5.464A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 26 through 28 removed outlier: 5.464A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 345 " --> pdb=" O GLY H 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AB3, first strand: chain 'H' and resid 185 through 191 removed outlier: 3.563A pdb=" N HIS H 204 " --> pdb=" O ALA H 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 26 through 29 removed outlier: 6.004A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 26 through 29 removed outlier: 6.004A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 268 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 345 " --> pdb=" O GLY I 324 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 185 through 190 Processing sheet with id=AB7, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.452A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 26 through 29 removed outlier: 5.452A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP J 326 " --> pdb=" O ILE J 347 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 184 through 190 removed outlier: 3.731A pdb=" N PHE J 189 " --> pdb=" O GLY J 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY J 206 " --> pdb=" O PHE J 189 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 26 through 29 removed outlier: 5.190A pdb=" N SER K 35 " --> pdb=" O SER K 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 26 through 29 removed outlier: 5.190A pdb=" N SER K 35 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE K 273 " --> pdb=" O ILE K 323 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE K 323 " --> pdb=" O PHE K 273 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 345 " --> pdb=" O GLY K 324 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 58 through 61 Processing sheet with id=AC4, first strand: chain 'K' and resid 147 through 148 Processing sheet with id=AC5, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.924A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.924A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 268 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TRP G 326 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 185 through 188 Processing sheet with id=AC8, first strand: chain 'B' and resid 7 through 13 removed outlier: 6.697A pdb=" N SER B 136 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N MET B 68 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG B 74 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N ILE B 207 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 236 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 243 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG B 245 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 232 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 247 " --> pdb=" O HIS B 230 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N HIS B 230 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ARG B 249 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLU B 228 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AD1, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AD2, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AD3, first strand: chain 'D' and resid 66 through 71 removed outlier: 4.191A pdb=" N VAL D 84 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 5 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 108 " --> pdb=" O ARG D 6 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AD5, first strand: chain 'D' and resid 125 through 127 removed outlier: 7.142A pdb=" N GLU D 233 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 191 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 132 through 137 Processing sheet with id=AD7, first strand: chain 'D' and resid 197 through 199 1084 hydrogen bonds defined for protein. 2997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7769 1.33 - 1.46: 6937 1.46 - 1.58: 13279 1.58 - 1.71: 183 1.71 - 1.83: 167 Bond restraints: 28335 Sorted by residual: bond pdb=" CB PRO H 321 " pdb=" CG PRO H 321 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.20e+00 bond pdb=" CB PRO B 145 " pdb=" CG PRO B 145 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.52e+00 bond pdb=" CB GLU I 198 " pdb=" CG GLU I 198 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.16e+00 bond pdb=" C VAL C 305 " pdb=" N PRO C 306 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.32e+00 bond pdb=" CB LYS F 341 " pdb=" CG LYS F 341 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.13e+00 ... (remaining 28330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 38376 3.76 - 7.52: 403 7.52 - 11.28: 63 11.28 - 15.04: 16 15.04 - 18.80: 5 Bond angle restraints: 38863 Sorted by residual: angle pdb=" CA LYS E 57 " pdb=" CB LYS E 57 " pdb=" CG LYS E 57 " ideal model delta sigma weight residual 114.10 127.03 -12.93 2.00e+00 2.50e-01 4.18e+01 angle pdb=" CB MET I 99 " pdb=" CG MET I 99 " pdb=" SD MET I 99 " ideal model delta sigma weight residual 112.70 129.67 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" CA PRO B 145 " pdb=" N PRO B 145 " pdb=" CD PRO B 145 " ideal model delta sigma weight residual 112.00 104.17 7.83 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO H 321 " pdb=" N PRO H 321 " pdb=" CD PRO H 321 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CB LYS H 292 " pdb=" CG LYS H 292 " pdb=" CD LYS H 292 " ideal model delta sigma weight residual 111.30 123.75 -12.45 2.30e+00 1.89e-01 2.93e+01 ... (remaining 38858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 15992 35.52 - 71.04: 908 71.04 - 106.56: 59 106.56 - 142.08: 1 142.08 - 177.60: 4 Dihedral angle restraints: 16964 sinusoidal: 7414 harmonic: 9550 Sorted by residual: dihedral pdb=" O4' C A 6 " pdb=" C1' C A 6 " pdb=" N1 C A 6 " pdb=" C2 C A 6 " ideal model delta sinusoidal sigma weight residual 200.00 57.79 142.21 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' C A 24 " pdb=" C1' C A 24 " pdb=" N1 C A 24 " pdb=" C2 C A 24 " ideal model delta sinusoidal sigma weight residual 200.00 72.96 127.04 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' U A 36 " pdb=" C1' U A 36 " pdb=" N1 U A 36 " pdb=" C2 U A 36 " ideal model delta sinusoidal sigma weight residual -128.00 49.60 -177.60 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 16961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3990 0.087 - 0.175: 318 0.175 - 0.262: 18 0.262 - 0.349: 3 0.349 - 0.437: 1 Chirality restraints: 4330 Sorted by residual: chirality pdb=" CB VAL C 305 " pdb=" CA VAL C 305 " pdb=" CG1 VAL C 305 " pdb=" CG2 VAL C 305 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE C 157 " pdb=" CA ILE C 157 " pdb=" CG1 ILE C 157 " pdb=" CG2 ILE C 157 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU B 60 " pdb=" CB LEU B 60 " pdb=" CD1 LEU B 60 " pdb=" CD2 LEU B 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 4327 not shown) Planarity restraints: 4735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 150 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO J 151 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO J 151 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO J 151 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 320 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO K 321 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO K 321 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO K 321 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 144 " 0.086 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO B 145 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.066 5.00e-02 4.00e+02 ... (remaining 4732 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3033 2.75 - 3.29: 26194 3.29 - 3.82: 48556 3.82 - 4.36: 55722 4.36 - 4.90: 94777 Nonbonded interactions: 228282 Sorted by model distance: nonbonded pdb=" O PRO I 266 " pdb=" OH TYR J 315 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C 182 " pdb=" OG SER C 326 " model vdw 2.226 3.040 nonbonded pdb=" O PHE K 189 " pdb=" NZ LYS D 110 " model vdw 2.244 3.120 nonbonded pdb=" OH TYR F 315 " pdb=" O PRO G 266 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP F 295 " pdb=" OH TYR F 333 " model vdw 2.260 3.040 ... (remaining 228277 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 'F' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 78 or (resid 79 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 86 or (resid 87 and (name N or name CA or name C or \ name O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 117 or (r \ esid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 o \ r (resid 120 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 21 or (resid 122 through 126 and (name N or name CA or name C or name O or name \ CB )) or resid 127 through 155 or (resid 156 and (name N or name CA or name C or \ name O or name CB )) or resid 157 through 159 or (resid 160 through 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 190 or re \ sid 208 through 225 or (resid 226 and (name N or name CA or name C or name O or \ name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 256 or resid 263 through 291 \ or (resid 292 and (name N or name CA or name C or name O or name CB )) or resid \ 293 through 315 or (resid 316 through 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 338 or (resid 339 and (name N or name C \ A or name C or name O or name CB )) or resid 340 or (resid 341 and (name N or na \ me CA or name C or name O or name CB )) or resid 342 through 351 or (resid 352 a \ nd (name N or name CA or name C or name O or name CB )) or resid 353 through 368 \ or (resid 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'H' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 121 or (resid 122 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 1 \ 59 or (resid 160 through 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 190 or resid 208 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and (n \ ame N or name CA or name C or name O or name CB )) or resid 229 through 230 or ( \ resid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 256 or resid 263 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O or name CB )) or resid 293 through 311 or (resid 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 316 or (resid 3 \ 17 through 319 and (name N or name CA or name C or name O or name CB )) or resid \ 320 through 338 or (resid 339 and (name N or name CA or name C or name O or nam \ e CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or \ name CB )) or resid 342 through 351 or (resid 352 and (name N or name CA or nam \ e C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB )) or resid 366 through 367 or (resid 3 \ 68 through 369 and (name N or name CA or name C or name O or name CB )) or resid \ 370 through 372)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (nam \ e N or name CA or name C or name O or name CB )) or resid 76 through 78 or (resi \ d 79 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or re \ sid 84 through 86 or (resid 87 and (name N or name CA or name C or name O or nam \ e CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N \ or name CA or name C or name O or name CB )) or resid 100 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 117 or (resid 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 or (resid 120 and (name N or name CA or name C or nam \ e O or name CB )) or resid 121 through 159 or (resid 160 through 161 and (name N \ or name CA or name C or name O or name CB )) or resid 162 through 190 or resid \ 208 through 225 or (resid 226 and (name N or name CA or name C or name O or name \ CB )) or resid 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 through 256 or resid 263 through 311 or (resid 312 and ( \ name N or name CA or name C or name O or name CB )) or resid 313 through 315 or \ (resid 316 through 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 338 or (resid 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 through 351 or (resid 352 and (name N or name CA or \ name C or name O or name CB )) or resid 353 through 364 or (resid 365 and (name \ N or name CA or name C or name O or name CB )) or resid 366 through 367 or (res \ id 368 through 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 or (resid 371 and (name N or name CA or name C or name O or name CB )) \ or resid 372)) selection = (chain 'J' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or na \ me O or name CB )) or resid 92 or resid 97 through 98 or (resid 99 and (name N o \ r name CA or name C or name O or name CB )) or resid 100 through 108 or (resid 1 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 110 through \ 121 or (resid 122 through 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 152 or (resid 153 through 154 and (name N or name C \ A or name C or name O or name CB )) or resid 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 through 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 190 \ or resid 208 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 through 230 or (resid 231 and (name N or name CA o \ r name C or name O or name CB )) or resid 232 through 256 or resid 263 through 3 \ 11 or (resid 312 and (name N or name CA or name C or name O or name CB )) or res \ id 313 through 315 or (resid 316 through 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 through 367 or (resid 368 thr \ ough 369 and (name N or name CA or name C or name O or name CB )) or resid 370 o \ r (resid 371 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 72)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 92 or resid 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 108 or ( \ resid 109 and (name N or name CA or name C or name O or name CB )) or resid 110 \ through 117 or (resid 118 and (name N or name CA or name C or name O or name CB \ )) or resid 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 or (resid 122 through 126 and (name N or name CA or name C o \ r name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and (n \ ame N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 an \ d (name N or name CA or name C or name O or name CB )) or resid 157 through 159 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 227 or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 311 or (resid 312 and (n \ ame N or name CA or name C or name O or name CB )) or resid 313 through 316 or ( \ resid 317 through 319 and (name N or name CA or name C or name O or name CB )) o \ r resid 320 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 or (resid 341 and (name N or name CA or name C or na \ me O or name CB )) or resid 342 through 367 or (resid 368 through 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 372)) } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.770 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.005 0.134 28335 Z= 0.205 Angle : 0.981 18.796 38863 Z= 0.489 Chirality : 0.049 0.437 4330 Planarity : 0.008 0.132 4735 Dihedral : 20.129 177.597 10798 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.29 % Favored : 92.50 % Rotamer: Outliers : 3.92 % Allowed : 35.39 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.14), residues: 3266 helix: -0.73 (0.14), residues: 1141 sheet: 0.31 (0.22), residues: 504 loop : -2.02 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG G 286 TYR 0.031 0.002 TYR G 188 PHE 0.036 0.002 PHE F 244 TRP 0.040 0.002 TRP E 156 HIS 0.007 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00485 (28335) covalent geometry : angle 0.98098 (38863) hydrogen bonds : bond 0.15526 ( 1068) hydrogen bonds : angle 6.22880 ( 3065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 394 time to evaluate : 1.057 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: C 477 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6333 (t80) REVERT: F 342 LEU cc_start: 0.7290 (tm) cc_final: 0.7061 (mt) REVERT: J 88 CYS cc_start: 0.8474 (t) cc_final: 0.8266 (m) REVERT: K 280 TYR cc_start: 0.8069 (m-10) cc_final: 0.7634 (m-10) REVERT: G 172 GLN cc_start: 0.8600 (pm20) cc_final: 0.8255 (pm20) outliers start: 105 outliers final: 84 residues processed: 484 average time/residue: 0.5311 time to fit residues: 305.8562 Evaluate side-chains 461 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 376 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 TRP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 234 THR Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 20 ASP Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 294 SER Chi-restraints excluded: chain J residue 328 SER Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 341 LYS Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN C 203 HIS I 17 ASN ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.075580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062153 restraints weight = 84436.171| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.73 r_work: 0.3008 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 28335 Z= 0.152 Angle : 0.672 11.858 38863 Z= 0.342 Chirality : 0.042 0.221 4330 Planarity : 0.006 0.131 4735 Dihedral : 16.672 177.151 4982 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 5.41 % Allowed : 29.38 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.14), residues: 3266 helix: 0.13 (0.15), residues: 1165 sheet: 0.24 (0.22), residues: 534 loop : -1.87 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 286 TYR 0.014 0.001 TYR H 360 PHE 0.019 0.001 PHE G 52 TRP 0.015 0.001 TRP E 46 HIS 0.003 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00353 (28335) covalent geometry : angle 0.67239 (38863) hydrogen bonds : bond 0.04372 ( 1068) hydrogen bonds : angle 4.75431 ( 3065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 392 time to evaluate : 1.236 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: C 259 MET cc_start: 0.6931 (tpt) cc_final: 0.6625 (tpt) REVERT: C 358 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8454 (pp) REVERT: C 477 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6548 (t80) REVERT: E 116 MET cc_start: 0.8404 (tmm) cc_final: 0.8177 (tmm) REVERT: F 44 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.7502 (tpm170) REVERT: F 245 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8963 (tt) REVERT: F 293 GLU cc_start: 0.7508 (pm20) cc_final: 0.7300 (pp20) REVERT: H 138 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8827 (tm) REVERT: H 164 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8739 (t0) REVERT: I 44 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8847 (ttp80) REVERT: I 152 ASN cc_start: 0.7697 (t0) cc_final: 0.7489 (t0) REVERT: J 88 CYS cc_start: 0.7869 (t) cc_final: 0.7412 (t) REVERT: J 103 MET cc_start: 0.7611 (pp-130) cc_final: 0.7229 (pp-130) REVERT: J 155 ASP cc_start: 0.7584 (t0) cc_final: 0.7310 (t0) REVERT: G 209 MET cc_start: 0.8861 (mtp) cc_final: 0.8631 (mtm) REVERT: B 237 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 299 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: D 101 ASP cc_start: 0.8185 (t0) cc_final: 0.7832 (t0) outliers start: 145 outliers final: 51 residues processed: 507 average time/residue: 0.5898 time to fit residues: 351.8519 Evaluate side-chains 433 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 373 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 TRP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 145 CYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 109 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 197 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 HIS E 132 GLN ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058925 restraints weight = 84656.854| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.68 r_work: 0.2932 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28335 Z= 0.203 Angle : 0.710 11.296 38863 Z= 0.360 Chirality : 0.044 0.296 4330 Planarity : 0.005 0.133 4735 Dihedral : 16.533 177.312 4895 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.65 % Favored : 92.13 % Rotamer: Outliers : 5.45 % Allowed : 29.71 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3266 helix: 0.39 (0.15), residues: 1154 sheet: 0.35 (0.22), residues: 522 loop : -1.81 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 113 TYR 0.014 0.001 TYR G 188 PHE 0.023 0.002 PHE B 237 TRP 0.016 0.001 TRP E 46 HIS 0.005 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00469 (28335) covalent geometry : angle 0.71019 (38863) hydrogen bonds : bond 0.04417 ( 1068) hydrogen bonds : angle 4.65605 ( 3065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 383 time to evaluate : 0.841 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: C 150 LYS cc_start: 0.8445 (tptp) cc_final: 0.8154 (tptp) REVERT: C 221 LYS cc_start: 0.7666 (pttp) cc_final: 0.7423 (pttm) REVERT: C 358 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8578 (pp) REVERT: C 471 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: F 44 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7992 (tpm170) REVERT: H 164 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8745 (t0) REVERT: I 293 GLU cc_start: 0.8377 (pm20) cc_final: 0.8138 (pp20) REVERT: J 88 CYS cc_start: 0.8050 (t) cc_final: 0.7624 (t) REVERT: J 103 MET cc_start: 0.7651 (pp-130) cc_final: 0.7168 (pp-130) REVERT: J 367 GLU cc_start: 0.8110 (tp30) cc_final: 0.7790 (tp30) REVERT: K 209 MET cc_start: 0.7075 (tpp) cc_final: 0.6110 (tpp) REVERT: K 322 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8781 (p) REVERT: K 337 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.7151 (t80) REVERT: G 172 GLN cc_start: 0.8726 (pp30) cc_final: 0.8475 (pp30) REVERT: B 48 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9263 (mmm) REVERT: B 237 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6936 (t80) REVERT: D 66 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7652 (tt) REVERT: D 101 ASP cc_start: 0.8384 (t0) cc_final: 0.8028 (t0) outliers start: 146 outliers final: 59 residues processed: 497 average time/residue: 0.6137 time to fit residues: 360.3567 Evaluate side-chains 426 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 358 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 TRP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 96 ASN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 71 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 HIS E 132 GLN ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060314 restraints weight = 84486.217| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.67 r_work: 0.2968 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28335 Z= 0.150 Angle : 0.674 10.965 38863 Z= 0.340 Chirality : 0.042 0.246 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.442 177.780 4884 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.32 % Favored : 92.50 % Rotamer: Outliers : 5.00 % Allowed : 30.61 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3266 helix: 0.50 (0.15), residues: 1169 sheet: 0.32 (0.22), residues: 522 loop : -1.80 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 154 TYR 0.012 0.001 TYR G 28 PHE 0.022 0.001 PHE B 237 TRP 0.015 0.001 TRP C 264 HIS 0.003 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00351 (28335) covalent geometry : angle 0.67377 (38863) hydrogen bonds : bond 0.03826 ( 1068) hydrogen bonds : angle 4.53156 ( 3065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 393 time to evaluate : 0.849 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: C 221 LYS cc_start: 0.7732 (pttp) cc_final: 0.7388 (pttm) REVERT: C 338 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7677 (p-90) REVERT: C 471 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8244 (ttm) REVERT: E 114 MET cc_start: 0.6777 (pmm) cc_final: 0.6522 (ppp) REVERT: F 44 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8354 (tpm170) REVERT: H 138 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7823 (tp) REVERT: H 157 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8368 (t0) REVERT: H 164 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (t0) REVERT: I 152 ASN cc_start: 0.7604 (t0) cc_final: 0.7389 (t0) REVERT: J 88 CYS cc_start: 0.8022 (t) cc_final: 0.7604 (t) REVERT: J 94 ASP cc_start: 0.7375 (p0) cc_final: 0.7141 (p0) REVERT: J 103 MET cc_start: 0.7590 (pp-130) cc_final: 0.7363 (pp-130) REVERT: J 217 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8861 (mttp) REVERT: J 250 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8436 (pttm) REVERT: J 367 GLU cc_start: 0.8115 (tp30) cc_final: 0.7769 (tp30) REVERT: K 322 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8752 (p) REVERT: K 323 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8489 (mp) REVERT: K 337 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.7119 (t80) REVERT: G 172 GLN cc_start: 0.8603 (pp30) cc_final: 0.8401 (pp30) REVERT: G 250 LYS cc_start: 0.8228 (ptpp) cc_final: 0.8009 (mtmm) REVERT: B 48 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.9244 (mmm) REVERT: B 237 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 313 TYR cc_start: 0.8664 (m-80) cc_final: 0.8427 (m-80) REVERT: D 66 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7678 (tt) REVERT: D 101 ASP cc_start: 0.8364 (t0) cc_final: 0.8052 (t0) REVERT: D 174 TRP cc_start: 0.8900 (t-100) cc_final: 0.8567 (t-100) outliers start: 134 outliers final: 52 residues processed: 499 average time/residue: 0.5978 time to fit residues: 351.0425 Evaluate side-chains 436 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 370 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 338 TRP Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 47 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN C 203 HIS ** I 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 339 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.059597 restraints weight = 84455.089| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.66 r_work: 0.2950 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 28335 Z= 0.166 Angle : 0.699 11.318 38863 Z= 0.351 Chirality : 0.043 0.222 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.392 177.600 4877 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.76 % Rotamer: Outliers : 5.30 % Allowed : 31.17 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 3266 helix: 0.58 (0.15), residues: 1172 sheet: 0.33 (0.22), residues: 531 loop : -1.78 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 286 TYR 0.016 0.001 TYR G 188 PHE 0.023 0.001 PHE B 237 TRP 0.016 0.001 TRP E 46 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00392 (28335) covalent geometry : angle 0.69949 (38863) hydrogen bonds : bond 0.03885 ( 1068) hydrogen bonds : angle 4.48376 ( 3065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 385 time to evaluate : 1.089 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: C 210 TYR cc_start: 0.7707 (m-10) cc_final: 0.7442 (m-10) REVERT: C 221 LYS cc_start: 0.7718 (pttp) cc_final: 0.7450 (pttm) REVERT: C 386 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7882 (ttt180) REVERT: C 471 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: E 114 MET cc_start: 0.6901 (pmm) cc_final: 0.6650 (pmm) REVERT: F 44 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8386 (tpm170) REVERT: H 1 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7864 (mmt) REVERT: H 138 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8067 (tp) REVERT: H 157 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8401 (t0) REVERT: H 164 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8722 (t0) REVERT: J 88 CYS cc_start: 0.8078 (t) cc_final: 0.7674 (t) REVERT: J 94 ASP cc_start: 0.7399 (p0) cc_final: 0.7166 (p0) REVERT: J 217 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8890 (mttp) REVERT: J 250 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8446 (pttm) REVERT: J 367 GLU cc_start: 0.8153 (tp30) cc_final: 0.7786 (tp30) REVERT: K 209 MET cc_start: 0.7208 (tpp) cc_final: 0.6118 (tpp) REVERT: K 317 ASP cc_start: 0.6232 (m-30) cc_final: 0.6013 (m-30) REVERT: K 322 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8757 (p) REVERT: K 323 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8523 (mp) REVERT: K 337 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.7205 (t80) REVERT: G 209 MET cc_start: 0.8945 (mtp) cc_final: 0.8664 (mtm) REVERT: G 293 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: B 30 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8320 (ptp90) REVERT: B 48 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9224 (mmm) REVERT: B 237 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7017 (t80) REVERT: D 37 MET cc_start: 0.6937 (tmm) cc_final: 0.6636 (mtp) REVERT: D 52 LEU cc_start: 0.8255 (tp) cc_final: 0.8039 (tp) REVERT: D 66 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7617 (tt) REVERT: D 101 ASP cc_start: 0.8409 (t0) cc_final: 0.8138 (t0) REVERT: D 135 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7961 (m-70) REVERT: D 174 TRP cc_start: 0.8868 (t-100) cc_final: 0.8570 (t-100) outliers start: 142 outliers final: 61 residues processed: 497 average time/residue: 0.6528 time to fit residues: 382.1207 Evaluate side-chains 451 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 HIS ** I 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058708 restraints weight = 84851.454| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.67 r_work: 0.2926 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 28335 Z= 0.182 Angle : 0.720 11.708 38863 Z= 0.362 Chirality : 0.044 0.237 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.403 177.516 4874 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.05 % Favored : 91.73 % Rotamer: Outliers : 5.04 % Allowed : 31.95 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 3266 helix: 0.61 (0.15), residues: 1165 sheet: 0.40 (0.23), residues: 516 loop : -1.76 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 113 TYR 0.018 0.001 TYR G 188 PHE 0.025 0.002 PHE B 237 TRP 0.017 0.001 TRP C 264 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00427 (28335) covalent geometry : angle 0.72015 (38863) hydrogen bonds : bond 0.04063 ( 1068) hydrogen bonds : angle 4.49404 ( 3065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 379 time to evaluate : 1.284 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: C 197 THR cc_start: 0.7123 (p) cc_final: 0.6807 (t) REVERT: C 471 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8287 (ttm) REVERT: F 44 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8378 (tpm170) REVERT: F 113 ARG cc_start: 0.7679 (mmm160) cc_final: 0.6987 (tpt90) REVERT: H 157 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8382 (t0) REVERT: H 164 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8727 (t0) REVERT: H 246 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8994 (mp) REVERT: J 88 CYS cc_start: 0.8115 (t) cc_final: 0.7697 (t) REVERT: J 250 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8425 (pttm) REVERT: J 367 GLU cc_start: 0.8185 (tp30) cc_final: 0.7779 (tp30) REVERT: K 322 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8690 (p) REVERT: K 323 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8560 (mp) REVERT: K 367 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8366 (tp30) REVERT: G 209 MET cc_start: 0.8998 (mtp) cc_final: 0.8773 (mtm) REVERT: G 293 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: B 30 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8517 (ptp90) REVERT: B 48 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9237 (mmm) REVERT: B 237 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7067 (t80) REVERT: B 282 GLU cc_start: 0.7399 (tp30) cc_final: 0.7166 (tp30) REVERT: B 284 LYS cc_start: 0.8984 (pptt) cc_final: 0.8690 (mttp) REVERT: D 34 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7906 (mmp80) REVERT: D 37 MET cc_start: 0.6965 (tmm) cc_final: 0.6177 (mtp) REVERT: D 66 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7635 (tt) REVERT: D 174 TRP cc_start: 0.8834 (t-100) cc_final: 0.8540 (t-100) REVERT: D 192 LEU cc_start: 0.7390 (pt) cc_final: 0.7128 (pp) outliers start: 135 outliers final: 62 residues processed: 486 average time/residue: 0.6745 time to fit residues: 384.2110 Evaluate side-chains 436 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 361 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 323 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 36 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN E 132 GLN F 10 ASN ** I 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057013 restraints weight = 84538.020| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.66 r_work: 0.2880 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 28335 Z= 0.229 Angle : 0.787 12.577 38863 Z= 0.396 Chirality : 0.046 0.237 4330 Planarity : 0.005 0.130 4735 Dihedral : 16.440 176.786 4869 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.27 % Favored : 91.55 % Rotamer: Outliers : 5.11 % Allowed : 32.92 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3266 helix: 0.48 (0.15), residues: 1161 sheet: 0.31 (0.22), residues: 525 loop : -1.80 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 113 TYR 0.023 0.002 TYR G 188 PHE 0.027 0.002 PHE B 237 TRP 0.022 0.002 TRP D 196 HIS 0.006 0.001 HIS G 180 Details of bonding type rmsd covalent geometry : bond 0.00534 (28335) covalent geometry : angle 0.78716 (38863) hydrogen bonds : bond 0.04434 ( 1068) hydrogen bonds : angle 4.60818 ( 3065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 371 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 THR cc_start: 0.7244 (p) cc_final: 0.6924 (t) REVERT: C 338 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7627 (p-90) REVERT: C 471 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8291 (ttm) REVERT: F 44 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8250 (tpm170) REVERT: H 164 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8776 (t0) REVERT: J 88 CYS cc_start: 0.8080 (t) cc_final: 0.7695 (t) REVERT: J 150 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6266 (pp20) REVERT: J 217 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8937 (mttp) REVERT: J 250 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8404 (pttm) REVERT: J 367 GLU cc_start: 0.8259 (tp30) cc_final: 0.7903 (tp30) REVERT: K 94 ASP cc_start: 0.8489 (t0) cc_final: 0.8276 (t70) REVERT: K 209 MET cc_start: 0.7370 (tpp) cc_final: 0.6144 (tpp) REVERT: K 317 ASP cc_start: 0.6584 (m-30) cc_final: 0.6356 (m-30) REVERT: K 337 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7274 (t80) REVERT: K 367 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8346 (tp30) REVERT: G 223 TRP cc_start: 0.7736 (t-100) cc_final: 0.7480 (t-100) REVERT: G 293 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: B 48 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.9270 (mmm) REVERT: B 52 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7797 (mpt-90) REVERT: B 237 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.6977 (t80) REVERT: B 282 GLU cc_start: 0.7252 (tp30) cc_final: 0.7025 (tp30) REVERT: D 37 MET cc_start: 0.7001 (tmm) cc_final: 0.6128 (tmm) REVERT: D 52 LEU cc_start: 0.8440 (tp) cc_final: 0.8127 (tm) REVERT: D 66 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7018 (mp) REVERT: D 101 ASP cc_start: 0.8527 (t0) cc_final: 0.8296 (t0) REVERT: D 135 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8013 (m-70) REVERT: D 192 LEU cc_start: 0.7414 (pt) cc_final: 0.7213 (pp) outliers start: 137 outliers final: 65 residues processed: 478 average time/residue: 0.6765 time to fit residues: 379.4237 Evaluate side-chains 440 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 361 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 338 TRP Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 337 TYR Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 157 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 305 optimal weight: 0.0370 chunk 324 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** 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 = 0.3334 r_free = 0.3334 target = 0.070746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057742 restraints weight = 84948.028| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.68 r_work: 0.2903 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28335 Z= 0.190 Angle : 0.769 13.095 38863 Z= 0.386 Chirality : 0.045 0.242 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.427 176.596 4869 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.78 % Favored : 92.04 % Rotamer: Outliers : 4.18 % Allowed : 33.89 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 3266 helix: 0.48 (0.15), residues: 1178 sheet: 0.35 (0.23), residues: 501 loop : -1.81 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 312 TYR 0.022 0.001 TYR G 188 PHE 0.026 0.002 PHE B 237 TRP 0.023 0.001 TRP D 196 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00447 (28335) covalent geometry : angle 0.76913 (38863) hydrogen bonds : bond 0.04124 ( 1068) hydrogen bonds : angle 4.57782 ( 3065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 381 time to evaluate : 1.129 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: C 197 THR cc_start: 0.7198 (p) cc_final: 0.6884 (t) REVERT: C 471 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: F 44 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8310 (tpm170) REVERT: H 164 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8745 (t0) REVERT: J 88 CYS cc_start: 0.8117 (t) cc_final: 0.7723 (t) REVERT: J 217 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8935 (mttp) REVERT: J 250 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8396 (pttm) REVERT: J 367 GLU cc_start: 0.8307 (tp30) cc_final: 0.7973 (tp30) REVERT: K 317 ASP cc_start: 0.6537 (m-30) cc_final: 0.6288 (m-30) REVERT: K 322 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8850 (p) REVERT: K 367 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8373 (tp30) REVERT: B 48 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9248 (mmm) REVERT: B 128 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8418 (ttt-90) REVERT: B 237 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7024 (t80) REVERT: B 282 GLU cc_start: 0.7199 (tp30) cc_final: 0.6986 (tp30) REVERT: D 66 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7048 (mp) REVERT: D 101 ASP cc_start: 0.8520 (t0) cc_final: 0.8286 (t0) REVERT: D 257 SER cc_start: 0.6789 (OUTLIER) cc_final: 0.6184 (m) outliers start: 112 outliers final: 60 residues processed: 472 average time/residue: 0.6806 time to fit residues: 378.7246 Evaluate side-chains 427 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 356 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 239 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** 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 = 0.3373 r_free = 0.3373 target = 0.072516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.059440 restraints weight = 84285.095| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.68 r_work: 0.2944 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28335 Z= 0.157 Angle : 0.770 13.331 38863 Z= 0.383 Chirality : 0.044 0.236 4330 Planarity : 0.005 0.126 4735 Dihedral : 16.347 177.358 4869 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.65 % Favored : 92.16 % Rotamer: Outliers : 3.10 % Allowed : 35.13 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 3266 helix: 0.69 (0.16), residues: 1169 sheet: 0.36 (0.23), residues: 508 loop : -1.79 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 113 TYR 0.019 0.001 TYR G 188 PHE 0.032 0.001 PHE C 139 TRP 0.026 0.001 TRP E 156 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00375 (28335) covalent geometry : angle 0.76977 (38863) hydrogen bonds : bond 0.03759 ( 1068) hydrogen bonds : angle 4.47828 ( 3065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 377 time to evaluate : 0.845 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: C 147 GLU cc_start: 0.8074 (pm20) cc_final: 0.7813 (pm20) REVERT: C 150 LYS cc_start: 0.8325 (tptp) cc_final: 0.8124 (tppt) REVERT: C 197 THR cc_start: 0.7200 (p) cc_final: 0.6878 (t) REVERT: C 471 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8215 (ttm) REVERT: F 44 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8420 (tpm170) REVERT: J 88 CYS cc_start: 0.8003 (t) cc_final: 0.7602 (t) REVERT: J 103 MET cc_start: 0.7154 (pp-130) cc_final: 0.6913 (pp-130) REVERT: J 217 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8875 (mttp) REVERT: J 250 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8365 (pttm) REVERT: J 367 GLU cc_start: 0.8267 (tp30) cc_final: 0.7910 (tp30) REVERT: K 317 ASP cc_start: 0.6576 (m-30) cc_final: 0.6337 (m-30) REVERT: G 293 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: B 48 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9211 (mmm) REVERT: B 128 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8469 (ttt-90) REVERT: B 237 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7102 (t80) REVERT: B 282 GLU cc_start: 0.7171 (tp30) cc_final: 0.6953 (tp30) REVERT: D 23 LYS cc_start: 0.8686 (mptt) cc_final: 0.8170 (mppt) REVERT: D 37 MET cc_start: 0.6980 (tmm) cc_final: 0.6629 (mtp) REVERT: D 66 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.6885 (mp) REVERT: D 101 ASP cc_start: 0.8456 (t0) cc_final: 0.8249 (t0) REVERT: D 174 TRP cc_start: 0.8907 (t-100) cc_final: 0.8584 (t-100) outliers start: 83 outliers final: 53 residues processed: 445 average time/residue: 0.5652 time to fit residues: 296.1996 Evaluate side-chains 421 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 157 ASP Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 258 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 183 optimal weight: 0.0670 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** 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 = 0.3392 r_free = 0.3392 target = 0.073332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.060217 restraints weight = 84667.461| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.69 r_work: 0.2964 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28335 Z= 0.151 Angle : 0.771 13.797 38863 Z= 0.383 Chirality : 0.043 0.252 4330 Planarity : 0.005 0.125 4735 Dihedral : 16.275 177.845 4867 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.25 % Rotamer: Outliers : 2.76 % Allowed : 35.87 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.15), residues: 3266 helix: 0.79 (0.16), residues: 1163 sheet: 0.36 (0.23), residues: 511 loop : -1.78 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 312 TYR 0.019 0.001 TYR G 188 PHE 0.027 0.001 PHE F 244 TRP 0.033 0.001 TRP E 156 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00362 (28335) covalent geometry : angle 0.77067 (38863) hydrogen bonds : bond 0.03639 ( 1068) hydrogen bonds : angle 4.43417 ( 3065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 373 time to evaluate : 1.107 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: C 122 MET cc_start: 0.6809 (ptt) cc_final: 0.6574 (ptm) REVERT: C 147 GLU cc_start: 0.8006 (pm20) cc_final: 0.7676 (pm20) REVERT: C 150 LYS cc_start: 0.8284 (tptp) cc_final: 0.8025 (tppt) REVERT: C 197 THR cc_start: 0.7190 (p) cc_final: 0.6869 (t) REVERT: C 301 LEU cc_start: 0.6732 (tt) cc_final: 0.6014 (mm) REVERT: C 471 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: F 44 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8444 (tpm170) REVERT: J 88 CYS cc_start: 0.8003 (t) cc_final: 0.7610 (t) REVERT: J 217 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8858 (mttp) REVERT: J 250 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8382 (pttm) REVERT: J 367 GLU cc_start: 0.8271 (tp30) cc_final: 0.7947 (tp30) REVERT: J 373 LYS cc_start: 0.8259 (tmtt) cc_final: 0.8053 (tptp) REVERT: K 317 ASP cc_start: 0.6514 (m-30) cc_final: 0.6295 (m-30) REVERT: G 293 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: B 48 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9179 (mmm) REVERT: B 128 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8465 (ttt-90) REVERT: B 237 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7123 (t80) REVERT: B 282 GLU cc_start: 0.7145 (tp30) cc_final: 0.6938 (tp30) REVERT: D 23 LYS cc_start: 0.8653 (mptt) cc_final: 0.8065 (mppt) REVERT: D 63 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6276 (m) REVERT: D 66 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6869 (mp) REVERT: D 101 ASP cc_start: 0.8380 (t0) cc_final: 0.8175 (t0) REVERT: D 174 TRP cc_start: 0.8928 (t-100) cc_final: 0.8616 (t-100) outliers start: 74 outliers final: 49 residues processed: 435 average time/residue: 0.6948 time to fit residues: 357.0479 Evaluate side-chains 422 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 363 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 477 TYR Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 217 LYS Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 244 PHE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 322 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 278 optimal weight: 0.0870 chunk 232 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** 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 = 0.3360 r_free = 0.3360 target = 0.071747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058775 restraints weight = 84736.126| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.64 r_work: 0.2932 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 28335 Z= 0.181 Angle : 0.801 13.603 38863 Z= 0.398 Chirality : 0.044 0.239 4330 Planarity : 0.005 0.124 4735 Dihedral : 16.269 177.802 4865 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.14 % Favored : 91.67 % Rotamer: Outliers : 3.02 % Allowed : 35.54 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 3266 helix: 0.74 (0.16), residues: 1162 sheet: 0.33 (0.22), residues: 525 loop : -1.76 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 113 TYR 0.023 0.001 TYR G 188 PHE 0.031 0.002 PHE C 139 TRP 0.037 0.002 TRP E 156 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00432 (28335) covalent geometry : angle 0.80091 (38863) hydrogen bonds : bond 0.03941 ( 1068) hydrogen bonds : angle 4.47174 ( 3065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8294.31 seconds wall clock time: 142 minutes 52.92 seconds (8572.92 seconds total)