Starting phenix.real_space_refine on Mon May 26 02:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp7_60328/05_2025/8zp7_60328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp7_60328/05_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_60328/05_2025/8zp7_60328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp7_60328/05_2025/8zp7_60328.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp7_60328/05_2025/8zp7_60328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp7_60328/05_2025/8zp7_60328.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP: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, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 1, 'ARG:plan': 2} 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: 17.01, per 1000 atoms: 0.62 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: 7.14 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 9.21 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: 9.59 Time building geometry restraints manager: 8.15 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 66.470 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.590 ------------------------------------------------------------------------------- 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 : 8.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (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 TRP 0.040 0.002 TRP E 156 HIS 0.007 0.001 HIS B 295 PHE 0.036 0.002 PHE F 244 TYR 0.031 0.002 TYR G 188 ARG 0.030 0.001 ARG G 286 Details of bonding type rmsd hydrogen bonds : bond 0.15526 ( 1068) hydrogen bonds : angle 6.22880 ( 3065) covalent geometry : bond 0.00485 (28335) covalent geometry : angle 0.98098 (38863) *********************** 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 : 2.941 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: 1.2130 time to fit residues: 704.7367 Evaluate side-chains 462 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 377 time to evaluate : 2.917 ------------------------------------------------------------------------------- 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 282 optimal weight: 5.9990 chunk 253 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 261 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** 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 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061326 restraints weight = 84033.888| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.74 r_work: 0.2987 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1113 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= 0.165 Angle : 0.679 11.895 38863 Z= 0.346 Chirality : 0.043 0.220 4330 Planarity : 0.006 0.132 4735 Dihedral : 16.685 177.080 4982 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.41 % Favored : 92.38 % Rotamer: Outliers : 5.45 % Allowed : 29.56 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3266 helix: 0.12 (0.15), residues: 1166 sheet: 0.24 (0.22), residues: 534 loop : -1.86 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 199 HIS 0.003 0.001 HIS G 180 PHE 0.020 0.002 PHE G 52 TYR 0.013 0.001 TYR H 360 ARG 0.008 0.001 ARG H 286 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 1068) hydrogen bonds : angle 4.73862 ( 3065) covalent geometry : bond 0.00384 (28335) covalent geometry : angle 0.67884 (38863) *********************** 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: 146 poor density : 391 time to evaluate : 3.114 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 259 MET cc_start: 0.6917 (tpt) cc_final: 0.6610 (tpt) REVERT: C 358 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8476 (pp) REVERT: C 477 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6549 (t80) REVERT: E 116 MET cc_start: 0.8371 (tmm) cc_final: 0.8147 (tmm) REVERT: E 118 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: F 44 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.7608 (tpm170) REVERT: F 245 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8978 (tt) REVERT: H 138 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8893 (tm) REVERT: I 44 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8839 (ttp80) REVERT: I 152 ASN cc_start: 0.7741 (t0) cc_final: 0.7525 (t0) REVERT: J 71 GLU cc_start: 0.7535 (pp20) cc_final: 0.7296 (pp20) REVERT: J 88 CYS cc_start: 0.7876 (t) cc_final: 0.7437 (t) REVERT: J 103 MET cc_start: 0.7649 (pp-130) cc_final: 0.7202 (pp-130) REVERT: J 155 ASP cc_start: 0.7629 (t0) cc_final: 0.7366 (t0) REVERT: G 209 MET cc_start: 0.8887 (mtp) cc_final: 0.8618 (mtm) REVERT: B 237 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 299 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: D 101 ASP cc_start: 0.8222 (t0) cc_final: 0.7878 (t0) outliers start: 146 outliers final: 56 residues processed: 507 average time/residue: 1.2332 time to fit residues: 742.3187 Evaluate side-chains 430 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 365 time to evaluate : 3.078 ------------------------------------------------------------------------------- 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 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 118 GLU 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 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 122 LEU Chi-restraints excluded: chain H residue 138 LEU 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 77 CYS 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 141 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 286 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 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 30 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** D 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059126 restraints weight = 84375.106| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.67 r_work: 0.2938 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1470 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= 0.193 Angle : 0.698 11.136 38863 Z= 0.355 Chirality : 0.043 0.296 4330 Planarity : 0.005 0.133 4735 Dihedral : 16.527 177.346 4895 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.65 % Favored : 92.16 % Rotamer: Outliers : 5.52 % Allowed : 29.60 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3266 helix: 0.38 (0.15), residues: 1163 sheet: 0.35 (0.22), residues: 522 loop : -1.84 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 46 HIS 0.004 0.001 HIS D 154 PHE 0.023 0.002 PHE B 237 TYR 0.012 0.001 TYR G 216 ARG 0.008 0.001 ARG H 286 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1068) hydrogen bonds : angle 4.62689 ( 3065) covalent geometry : bond 0.00445 (28335) covalent geometry : angle 0.69834 (38863) *********************** 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 536 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 388 time to evaluate : 3.213 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: C 325 CYS cc_start: 0.6365 (OUTLIER) cc_final: 0.6144 (p) REVERT: C 358 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8530 (pp) REVERT: F 44 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.7973 (tpm170) REVERT: H 138 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9016 (tm) REVERT: J 88 CYS cc_start: 0.8028 (t) cc_final: 0.7611 (t) REVERT: J 103 MET cc_start: 0.7690 (pp-130) cc_final: 0.7215 (pp-130) REVERT: J 367 GLU cc_start: 0.8105 (tp30) cc_final: 0.7666 (tp30) REVERT: K 209 MET cc_start: 0.7070 (tpp) cc_final: 0.6093 (tpp) REVERT: K 322 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8802 (p) REVERT: K 337 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7239 (t80) REVERT: G 172 GLN cc_start: 0.8713 (pp30) cc_final: 0.8457 (pp30) REVERT: B 48 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9258 (mmm) REVERT: B 237 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6950 (t80) REVERT: D 66 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7657 (tt) REVERT: D 101 ASP cc_start: 0.8384 (t0) cc_final: 0.8056 (t0) outliers start: 148 outliers final: 60 residues processed: 504 average time/residue: 1.2457 time to fit residues: 751.4082 Evaluate side-chains 434 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 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 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 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 165 THR 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 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 77 CYS 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 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 B residue 341 TYR 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 26 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 290 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 152 optimal weight: 0.0870 chunk 180 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 F 17 ASN ** I 17 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061704 restraints weight = 84884.174| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.69 r_work: 0.3004 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 28335 Z= 0.130 Angle : 0.661 11.014 38863 Z= 0.332 Chirality : 0.042 0.247 4330 Planarity : 0.005 0.128 4735 Dihedral : 16.405 177.617 4884 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.32 % Favored : 92.50 % Rotamer: Outliers : 4.85 % Allowed : 30.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3266 helix: 0.61 (0.16), residues: 1161 sheet: 0.33 (0.22), residues: 520 loop : -1.77 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 264 HIS 0.003 0.001 HIS C 206 PHE 0.020 0.001 PHE B 237 TYR 0.013 0.001 TYR G 28 ARG 0.009 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 1068) hydrogen bonds : angle 4.45771 ( 3065) covalent geometry : bond 0.00306 (28335) covalent geometry : angle 0.66118 (38863) *********************** 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 531 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 401 time to evaluate : 2.970 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: 0.7669 (m-10) cc_final: 0.7462 (m-10) REVERT: C 221 LYS cc_start: 0.7598 (pttp) cc_final: 0.7286 (pttm) REVERT: C 471 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8261 (ttm) REVERT: C 477 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6488 (t80) REVERT: F 44 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8385 (tpm170) REVERT: H 138 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8954 (tm) REVERT: H 157 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8355 (t0) REVERT: J 88 CYS cc_start: 0.7966 (t) cc_final: 0.7544 (t) REVERT: J 103 MET cc_start: 0.7536 (pp-130) cc_final: 0.7226 (pp-130) REVERT: J 217 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8852 (mttp) REVERT: J 367 GLU cc_start: 0.8075 (tp30) cc_final: 0.7713 (tp30) REVERT: K 209 MET cc_start: 0.6881 (tpp) cc_final: 0.6045 (tpp) REVERT: K 322 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8718 (p) REVERT: K 323 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8373 (mp) REVERT: G 250 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7982 (mtmm) REVERT: B 237 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7066 (t80) REVERT: B 313 TYR cc_start: 0.8563 (m-80) cc_final: 0.8325 (m-80) REVERT: D 66 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (tt) REVERT: D 101 ASP cc_start: 0.8324 (t0) cc_final: 0.8035 (t0) REVERT: D 174 TRP cc_start: 0.8893 (t-100) cc_final: 0.8548 (t-100) outliers start: 130 outliers final: 46 residues processed: 504 average time/residue: 1.2207 time to fit residues: 730.3014 Evaluate side-chains 431 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 375 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 157 ASP Chi-restraints excluded: chain H residue 190 VAL 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 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 251 THR Chi-restraints excluded: chain J residue 290 VAL 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 350 LEU Chi-restraints excluded: chain B residue 17 GLN 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 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 253 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 166 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 304 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** 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 = 0.3363 r_free = 0.3363 target = 0.072037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058947 restraints weight = 84502.723| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.65 r_work: 0.2934 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1800 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= 0.189 Angle : 0.711 11.289 38863 Z= 0.360 Chirality : 0.043 0.225 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.394 177.402 4873 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 5.04 % Allowed : 31.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3266 helix: 0.62 (0.16), residues: 1164 sheet: 0.36 (0.22), residues: 530 loop : -1.77 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 46 HIS 0.005 0.001 HIS D 154 PHE 0.024 0.002 PHE B 237 TYR 0.016 0.001 TYR G 188 ARG 0.008 0.001 ARG J 113 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1068) hydrogen bonds : angle 4.48765 ( 3065) covalent geometry : bond 0.00441 (28335) covalent geometry : angle 0.71084 (38863) *********************** 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 531 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 396 time to evaluate : 2.910 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: C 221 LYS cc_start: 0.7671 (pttp) cc_final: 0.7329 (pttm) REVERT: C 471 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8347 (ttm) REVERT: F 44 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8320 (tpm170) REVERT: H 1 MET cc_start: 0.8166 (tpt) cc_final: 0.7938 (tpt) REVERT: H 138 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9025 (tm) REVERT: H 157 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8390 (t0) REVERT: J 88 CYS cc_start: 0.8113 (t) cc_final: 0.7724 (t) REVERT: J 94 ASP cc_start: 0.7421 (p0) cc_final: 0.7188 (p0) REVERT: J 250 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8418 (pttm) REVERT: J 367 GLU cc_start: 0.8212 (tp30) cc_final: 0.7855 (tp30) REVERT: K 322 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8701 (p) REVERT: K 337 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7189 (t80) REVERT: B 30 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8284 (ptp90) REVERT: B 237 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7024 (t80) REVERT: D 52 LEU cc_start: 0.8283 (tp) cc_final: 0.8030 (tp) REVERT: D 66 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7583 (tt) REVERT: D 101 ASP cc_start: 0.8418 (t0) cc_final: 0.8160 (t0) outliers start: 135 outliers final: 61 residues processed: 503 average time/residue: 1.2713 time to fit residues: 762.1457 Evaluate side-chains 443 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 372 time to evaluate : 3.048 ------------------------------------------------------------------------------- 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 295 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 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 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 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 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 190 VAL Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR 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 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 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 247 VAL 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 27 ASN Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 129 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 318 optimal weight: 1.9990 chunk 166 optimal weight: 0.0000 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 HIS K 96 ASN ** G 9 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.059523 restraints weight = 85018.598| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.67 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: 0.8459 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28335 Z= 0.163 Angle : 0.713 11.950 38863 Z= 0.358 Chirality : 0.043 0.242 4330 Planarity : 0.005 0.128 4735 Dihedral : 16.390 177.507 4873 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.31 % Rotamer: Outliers : 4.59 % Allowed : 33.00 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3266 helix: 0.65 (0.16), residues: 1166 sheet: 0.44 (0.23), residues: 512 loop : -1.78 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 264 HIS 0.003 0.001 HIS D 154 PHE 0.024 0.001 PHE B 237 TYR 0.016 0.001 TYR G 188 ARG 0.010 0.001 ARG J 113 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1068) hydrogen bonds : angle 4.45216 ( 3065) covalent geometry : bond 0.00385 (28335) covalent geometry : angle 0.71332 (38863) *********************** 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 510 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 387 time to evaluate : 2.920 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 197 THR cc_start: 0.7227 (p) cc_final: 0.6882 (t) REVERT: C 221 LYS cc_start: 0.7662 (pttp) cc_final: 0.7334 (pttm) REVERT: C 471 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: F 44 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8440 (tpm170) REVERT: F 113 ARG cc_start: 0.7549 (mmm160) cc_final: 0.7342 (tpt90) REVERT: H 138 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9011 (tm) REVERT: H 157 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8385 (t0) REVERT: J 88 CYS cc_start: 0.8084 (t) cc_final: 0.7663 (t) REVERT: J 94 ASP cc_start: 0.7389 (p0) cc_final: 0.7152 (p0) REVERT: J 217 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8901 (mttp) REVERT: J 250 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8404 (pttm) REVERT: J 367 GLU cc_start: 0.8217 (tp30) cc_final: 0.7903 (tp30) REVERT: K 209 MET cc_start: 0.7233 (tpp) cc_final: 0.6080 (tpp) REVERT: K 323 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8507 (mp) REVERT: G 293 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: B 237 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 282 GLU cc_start: 0.7381 (tp30) cc_final: 0.7137 (tp30) REVERT: B 284 LYS cc_start: 0.8972 (pptt) cc_final: 0.8672 (mttp) REVERT: B 313 TYR cc_start: 0.8762 (m-80) cc_final: 0.8561 (m-80) REVERT: D 37 MET cc_start: 0.6960 (tmm) cc_final: 0.6366 (mmp) REVERT: D 52 LEU cc_start: 0.8320 (tp) cc_final: 0.8021 (tp) REVERT: D 66 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7636 (tt) REVERT: D 174 TRP cc_start: 0.8869 (t-100) cc_final: 0.8521 (t-100) outliers start: 123 outliers final: 62 residues processed: 485 average time/residue: 1.2185 time to fit residues: 700.2798 Evaluate side-chains 439 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 367 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 192 ILE 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 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 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 338 LYS Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 117 ASP 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 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 340 SER 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 138 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 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 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 235 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 247 VAL 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 27 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 182 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 230 optimal weight: 0.0570 chunk 93 optimal weight: 6.9990 chunk 257 optimal weight: 0.0770 chunk 144 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.060969 restraints weight = 84397.446| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.68 r_work: 0.2982 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 28335 Z= 0.142 Angle : 0.716 12.530 38863 Z= 0.357 Chirality : 0.043 0.230 4330 Planarity : 0.005 0.126 4735 Dihedral : 16.308 177.131 4871 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.53 % Rotamer: Outliers : 4.40 % Allowed : 33.30 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3266 helix: 0.74 (0.16), residues: 1171 sheet: 0.40 (0.22), residues: 522 loop : -1.76 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 264 HIS 0.003 0.000 HIS B 333 PHE 0.023 0.001 PHE B 237 TYR 0.016 0.001 TYR G 188 ARG 0.010 0.001 ARG J 113 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1068) hydrogen bonds : angle 4.36325 ( 3065) covalent geometry : bond 0.00340 (28335) covalent geometry : angle 0.71623 (38863) *********************** 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 506 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 388 time to evaluate : 3.316 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 471 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8277 (ttm) REVERT: C 477 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6475 (t80) REVERT: E 156 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7036 (t60) REVERT: E 162 LYS cc_start: 0.9036 (ptpp) cc_final: 0.8835 (ptpp) REVERT: F 44 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8449 (tpm170) REVERT: F 111 LEU cc_start: 0.8628 (mm) cc_final: 0.8325 (mp) REVERT: H 138 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8989 (tm) REVERT: H 157 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8313 (t0) REVERT: H 246 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8852 (mp) REVERT: I 113 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6753 (mmt90) REVERT: J 88 CYS cc_start: 0.7948 (t) cc_final: 0.7536 (t) REVERT: J 94 ASP cc_start: 0.7362 (p0) cc_final: 0.7118 (p0) REVERT: J 217 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8839 (mttp) REVERT: J 250 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8367 (pttm) REVERT: J 367 GLU cc_start: 0.8250 (tp30) cc_final: 0.8021 (tp30) REVERT: K 209 MET cc_start: 0.7170 (tpp) cc_final: 0.6177 (tpp) REVERT: K 323 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8483 (mp) REVERT: G 223 TRP cc_start: 0.7544 (t-100) cc_final: 0.7324 (t-100) REVERT: G 250 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7994 (mppt) REVERT: G 293 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: B 30 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8364 (ptp90) REVERT: B 237 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 284 LYS cc_start: 0.8927 (pptt) cc_final: 0.8640 (mttp) REVERT: B 313 TYR cc_start: 0.8680 (m-80) cc_final: 0.8427 (m-80) REVERT: D 52 LEU cc_start: 0.8351 (tp) cc_final: 0.8024 (tp) REVERT: D 66 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.6902 (mp) REVERT: D 101 ASP cc_start: 0.8369 (t0) cc_final: 0.8153 (t0) REVERT: D 174 TRP cc_start: 0.8906 (t-100) cc_final: 0.8568 (t-100) outliers start: 118 outliers final: 61 residues processed: 484 average time/residue: 1.2675 time to fit residues: 726.4022 Evaluate side-chains 438 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 3.284 ------------------------------------------------------------------------------- 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 189 THR 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 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 91 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 156 TRP Chi-restraints excluded: chain F residue 32 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 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 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 138 LEU 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 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 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 211 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 B residue 354 ASP Chi-restraints excluded: chain D residue 27 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 254 optimal weight: 0.0980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 GLN F 10 ASN I 86 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN B 142 GLN ** D 30 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057452 restraints weight = 85393.401| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.69 r_work: 0.2893 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2179 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= 0.222 Angle : 0.794 12.898 38863 Z= 0.400 Chirality : 0.045 0.237 4330 Planarity : 0.006 0.129 4735 Dihedral : 16.409 176.808 4871 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 4.37 % Allowed : 33.78 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3266 helix: 0.59 (0.15), residues: 1153 sheet: 0.44 (0.23), residues: 514 loop : -1.75 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 196 HIS 0.005 0.001 HIS G 180 PHE 0.027 0.002 PHE B 237 TYR 0.023 0.002 TYR G 188 ARG 0.016 0.001 ARG K 312 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 1068) hydrogen bonds : angle 4.55242 ( 3065) covalent geometry : bond 0.00520 (28335) covalent geometry : angle 0.79352 (38863) *********************** 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 490 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 373 time to evaluate : 3.112 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: 0.8062 (pm20) cc_final: 0.7836 (pm20) REVERT: C 197 THR cc_start: 0.7145 (p) cc_final: 0.6838 (t) REVERT: C 471 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8354 (ttm) REVERT: F 44 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8306 (tpm170) REVERT: F 111 LEU cc_start: 0.8702 (mm) cc_final: 0.8384 (mp) REVERT: H 138 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9057 (tm) REVERT: I 113 ARG cc_start: 0.7189 (mtt90) cc_final: 0.6798 (mmt90) REVERT: J 88 CYS cc_start: 0.8146 (t) cc_final: 0.7746 (t) REVERT: J 94 ASP cc_start: 0.7419 (p0) cc_final: 0.7202 (p0) REVERT: J 217 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8963 (mttp) REVERT: J 250 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8441 (pttm) REVERT: J 367 GLU cc_start: 0.8348 (tp30) cc_final: 0.8012 (tp30) REVERT: K 1 MET cc_start: 0.8078 (ppp) cc_final: 0.7713 (ppp) REVERT: K 317 ASP cc_start: 0.6503 (m-30) cc_final: 0.6264 (m-30) REVERT: K 323 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8631 (mp) REVERT: K 337 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7246 (t80) REVERT: G 293 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: B 237 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 313 TYR cc_start: 0.8898 (m-80) cc_final: 0.8691 (m-80) REVERT: D 37 MET cc_start: 0.6893 (tmm) cc_final: 0.6493 (mtp) REVERT: D 192 LEU cc_start: 0.7307 (pt) cc_final: 0.7091 (pp) outliers start: 117 outliers final: 58 residues processed: 466 average time/residue: 1.3569 time to fit residues: 746.8547 Evaluate side-chains 423 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 3.060 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 356 ILE 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 102 LEU 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 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 96 ASN Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 138 LEU 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 155 ASP 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 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 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 240 THR 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 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 211 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 B residue 358 ARG Chi-restraints excluded: chain D residue 27 ASN 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 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 112 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057054 restraints weight = 84744.501| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.66 r_work: 0.2882 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 28335 Z= 0.229 Angle : 0.819 13.411 38863 Z= 0.413 Chirality : 0.046 0.239 4330 Planarity : 0.005 0.129 4735 Dihedral : 16.439 176.879 4870 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.18 % Favored : 91.64 % Rotamer: Outliers : 3.32 % Allowed : 35.16 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3266 helix: 0.43 (0.15), residues: 1172 sheet: 0.41 (0.23), residues: 499 loop : -1.82 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 196 HIS 0.005 0.001 HIS G 180 PHE 0.028 0.002 PHE B 237 TYR 0.025 0.002 TYR G 188 ARG 0.013 0.001 ARG J 113 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 1068) hydrogen bonds : angle 4.60761 ( 3065) covalent geometry : bond 0.00538 (28335) covalent geometry : angle 0.81853 (38863) *********************** 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 457 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 368 time to evaluate : 3.042 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: 0.7206 (p) cc_final: 0.6894 (t) REVERT: C 471 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: F 44 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8265 (tpm170) REVERT: F 111 LEU cc_start: 0.8728 (mm) cc_final: 0.8407 (mp) REVERT: I 113 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6887 (mmt90) REVERT: J 88 CYS cc_start: 0.8055 (t) cc_final: 0.7663 (t) REVERT: J 150 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6267 (pp20) REVERT: J 217 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8958 (mttp) REVERT: J 250 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8404 (pttm) REVERT: J 367 GLU cc_start: 0.8336 (tp30) cc_final: 0.7982 (tp30) REVERT: K 1 MET cc_start: 0.8055 (ppp) cc_final: 0.7717 (ppp) REVERT: K 337 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7316 (t80) REVERT: G 293 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: B 237 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.6971 (t80) REVERT: D 34 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7720 (mmp80) REVERT: D 37 MET cc_start: 0.6999 (tmm) cc_final: 0.6288 (mtp) REVERT: D 63 THR cc_start: 0.6904 (OUTLIER) cc_final: 0.6566 (m) REVERT: D 66 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7043 (mp) REVERT: D 101 ASP cc_start: 0.8535 (t0) cc_final: 0.8331 (t0) REVERT: D 257 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.6230 (m) outliers start: 89 outliers final: 58 residues processed: 445 average time/residue: 1.3070 time to fit residues: 687.1018 Evaluate side-chains 419 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 356 ILE 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 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 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 138 LEU 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 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 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 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 240 THR 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 125 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 211 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 27 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 234 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 256 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 196 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 96 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN G 351 ASN ** 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 = 0.3407 r_free = 0.3407 target = 0.074009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060926 restraints weight = 84122.419| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.68 r_work: 0.2983 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 28335 Z= 0.147 Angle : 0.779 13.843 38863 Z= 0.390 Chirality : 0.043 0.238 4330 Planarity : 0.005 0.125 4735 Dihedral : 16.337 177.767 4870 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.44 % Favored : 92.41 % Rotamer: Outliers : 2.65 % Allowed : 36.02 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3266 helix: 0.73 (0.16), residues: 1165 sheet: 0.39 (0.23), residues: 492 loop : -1.77 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 92 HIS 0.004 0.001 HIS I 204 PHE 0.023 0.001 PHE B 237 TYR 0.023 0.001 TYR C 300 ARG 0.014 0.001 ARG C 441 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1068) hydrogen bonds : angle 4.44557 ( 3065) covalent geometry : bond 0.00352 (28335) covalent geometry : angle 0.77870 (38863) ********************** 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 458 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 3.489 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 122 MET cc_start: 0.5631 (ptm) cc_final: 0.5356 (ptt) REVERT: C 197 THR cc_start: 0.7150 (p) cc_final: 0.6831 (t) REVERT: C 471 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8199 (ttm) REVERT: F 44 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8442 (tpm170) REVERT: H 138 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9025 (tm) REVERT: J 88 CYS cc_start: 0.8015 (t) cc_final: 0.7630 (t) REVERT: J 217 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8850 (mttp) REVERT: J 250 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8350 (pttm) REVERT: J 367 GLU cc_start: 0.8252 (tp30) cc_final: 0.7932 (tp30) REVERT: K 317 ASP cc_start: 0.6552 (m-30) cc_final: 0.6349 (m-30) REVERT: B 30 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8213 (ptp90) REVERT: B 237 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7045 (t80) REVERT: B 282 GLU cc_start: 0.6981 (tp30) cc_final: 0.6400 (tp30) REVERT: B 313 TYR cc_start: 0.8812 (m-80) cc_final: 0.8476 (m-80) REVERT: B 349 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6554 (mpt180) REVERT: D 23 LYS cc_start: 0.8669 (mptt) cc_final: 0.8191 (mppt) REVERT: D 34 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7694 (mmp80) REVERT: D 37 MET cc_start: 0.6933 (tmm) cc_final: 0.6276 (mtp) REVERT: D 63 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6235 (m) REVERT: D 66 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.6881 (mp) REVERT: D 174 TRP cc_start: 0.8882 (t-100) cc_final: 0.8596 (t-100) REVERT: D 257 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.5964 (m) outliers start: 71 outliers final: 42 residues processed: 443 average time/residue: 1.3711 time to fit residues: 724.1689 Evaluate side-chains 428 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 376 time to evaluate : 3.170 ------------------------------------------------------------------------------- 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 259 MET Chi-restraints excluded: chain C residue 356 ILE 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 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 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 138 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 97 THR 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 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 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 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 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 358 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 297 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS K 96 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.070468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057469 restraints weight = 84918.457| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.64 r_work: 0.2897 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2354 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= 0.219 Angle : 0.827 13.989 38863 Z= 0.417 Chirality : 0.045 0.229 4330 Planarity : 0.005 0.128 4735 Dihedral : 16.330 177.813 4868 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.27 % Favored : 91.58 % Rotamer: Outliers : 2.54 % Allowed : 36.69 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3266 helix: 0.63 (0.15), residues: 1163 sheet: 0.35 (0.22), residues: 518 loop : -1.78 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 92 HIS 0.009 0.001 HIS C 252 PHE 0.033 0.002 PHE C 139 TYR 0.025 0.002 TYR G 188 ARG 0.014 0.001 ARG K 312 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 1068) hydrogen bonds : angle 4.51685 ( 3065) covalent geometry : bond 0.00516 (28335) covalent geometry : angle 0.82719 (38863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17085.97 seconds wall clock time: 295 minutes 51.95 seconds (17751.95 seconds total)