Starting phenix.real_space_refine on Mon Aug 25 11:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2o_43753/08_2025/8w2o_43753.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 330 5.49 5 S 85 5.16 5 C 16628 2.51 5 N 4861 2.21 5 O 6213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28117 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1092 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 7, 'HIS:plan': 2, 'ASP:plan': 8, 'TYR:plan': 4, 'PHE:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 169 Chain: "B" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1462 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 4523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4523 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 529} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 3985 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ARG:plan': 11, 'ASP:plan': 14, 'GLN:plan1': 15, 'PHE:plan': 18, 'ASN:plan1': 19, 'TYR:plan': 10, 'TRP:plan': 9, 'GLU:plan': 16, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 552 Chain: "F" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1401 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 171} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1897 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 420 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "I" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 573 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 580 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 537 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "r" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "R" Number of atoms: 6937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 6937 Classifications: {'RNA': 327} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 26, 'rna3p_pur': 141, 'rna3p_pyr': 140} Link IDs: {'rna2p': 46, 'rna3p': 280} Chain breaks: 4 Time building chain proxies: 7.05, per 1000 atoms: 0.25 Number of scatterers: 28117 At special positions: 0 Unit cell: (145.25, 126.16, 237.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 330 15.00 O 6213 8.00 N 4861 7.00 C 16628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 989.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5272 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 52.5% alpha, 14.8% beta 106 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.937A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 87 removed outlier: 4.202A pdb=" N ARG A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'B' and resid 18 through 25 removed outlier: 3.605A pdb=" N LYS B 22 " --> pdb=" O PRO B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 48 removed outlier: 3.725A pdb=" N TYR B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.119A pdb=" N ASN B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 99 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.521A pdb=" N TYR B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.564A pdb=" N LYS B 117 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 4.299A pdb=" N VAL B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'C' and resid 15 through 28 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 134 through 147 removed outlier: 3.845A pdb=" N ARG C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 23 removed outlier: 4.018A pdb=" N SER D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 49 through 67 Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.519A pdb=" N PHE D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.174A pdb=" N ASN D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.617A pdb=" N TYR D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.895A pdb=" N LYS D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.878A pdb=" N PHE D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 202 Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 222 through 255 Processing helix chain 'D' and resid 272 through 290 removed outlier: 3.620A pdb=" N GLN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 306 through 309 removed outlier: 3.577A pdb=" N TYR D 309 " --> pdb=" O LEU D 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 326 through 341 removed outlier: 4.075A pdb=" N LYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 358 Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.598A pdb=" N LEU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 384 through 403 removed outlier: 4.094A pdb=" N PHE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 4.153A pdb=" N SER D 410 " --> pdb=" O TYR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 429 removed outlier: 4.069A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 446 removed outlier: 4.077A pdb=" N GLN D 446 " --> pdb=" O ASN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 468 removed outlier: 4.374A pdb=" N GLN D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS D 463 " --> pdb=" O ASN D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 475 through 488 removed outlier: 3.770A pdb=" N TRP D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 509 removed outlier: 4.618A pdb=" N TRP D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 513 through 529 Proline residue: D 519 - end of helix Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.762A pdb=" N ARG E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 87 through 101 Processing helix chain 'E' and resid 103 through 117 Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 134 removed outlier: 4.250A pdb=" N ALA E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 Proline residue: E 144 - end of helix removed outlier: 3.566A pdb=" N ASN E 155 " --> pdb=" O CYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 174 Processing helix chain 'E' and resid 176 through 189 Proline residue: E 187 - end of helix Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 213 through 240 removed outlier: 4.674A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 270 through 285 removed outlier: 4.627A pdb=" N ASP E 276 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 285 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 304 Processing helix chain 'E' and resid 306 through 321 removed outlier: 3.693A pdb=" N VAL E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 344 removed outlier: 5.043A pdb=" N ARG E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN E 343 " --> pdb=" O LYS E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 362 removed outlier: 3.701A pdb=" N ASN E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 380 Processing helix chain 'E' and resid 388 through 412 removed outlier: 3.510A pdb=" N GLU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.690A pdb=" N THR E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 444 removed outlier: 4.059A pdb=" N VAL E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 460 removed outlier: 4.369A pdb=" N LYS E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 466 removed outlier: 4.785A pdb=" N ASN E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 481 removed outlier: 3.557A pdb=" N TRP E 471 " --> pdb=" O SER E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 501 through 520 Processing helix chain 'E' and resid 521 through 529 Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 591 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'F' and resid 325 through 334 Processing helix chain 'F' and resid 357 through 368 Processing helix chain 'F' and resid 385 through 398 Processing helix chain 'F' and resid 500 through 519 removed outlier: 3.582A pdb=" N SER F 517 " --> pdb=" O LEU F 513 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN F 518 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 3.616A pdb=" N THR G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 94 removed outlier: 4.168A pdb=" N TYR G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 142 removed outlier: 3.581A pdb=" N CYS G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 142 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 220 Processing helix chain 'G' and resid 230 through 252 removed outlier: 3.554A pdb=" N TYR G 234 " --> pdb=" O ASN G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 257 removed outlier: 3.956A pdb=" N ILE G 256 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY G 257 " --> pdb=" O PRO G 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 257' Processing helix chain 'G' and resid 262 through 293 removed outlier: 3.673A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) Proline residue: G 272 - end of helix Processing helix chain 'H' and resid 8 through 14 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.528A pdb=" N LEU H 43 " --> pdb=" O PHE H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 52 Processing helix chain 'I' and resid 6 through 19 removed outlier: 4.214A pdb=" N GLU I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 104 through 132 removed outlier: 3.513A pdb=" N LYS K 132 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 8 removed outlier: 3.812A pdb=" N PHE L 6 " --> pdb=" O LYS L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 68 Processing helix chain 'L' and resid 109 through 119 Processing helix chain 'M' and resid 3 through 8 Processing helix chain 'M' and resid 14 through 28 Processing helix chain 'M' and resid 31 through 40 Processing helix chain 'N' and resid 6 through 14 Processing helix chain 'N' and resid 65 through 67 No H-bonds generated for 'chain 'N' and resid 65 through 67' Processing helix chain 'N' and resid 75 through 85 Proline residue: N 82 - end of helix removed outlier: 3.599A pdb=" N LYS N 85 " --> pdb=" O PRO N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 24 Processing helix chain 'P' and resid 14 through 22 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.935A pdb=" N LYS A 135 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 152 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 151 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A 110 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP A 184 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.823A pdb=" N PHE B 4 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 13 " --> pdb=" O PHE B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.725A pdb=" N VAL C 101 " --> pdb=" O ARG C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 576 through 577 removed outlier: 3.586A pdb=" N LYS E 615 " --> pdb=" O THR E 577 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 582 through 583 Processing sheet with id=AA9, first strand: chain 'F' and resid 339 through 343 removed outlier: 6.842A pdb=" N GLN F 354 " --> pdb=" O VAL F 340 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 342 " --> pdb=" O PHE F 352 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE F 352 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 444 through 446 Processing sheet with id=AB2, first strand: chain 'G' and resid 69 through 75 removed outlier: 4.532A pdb=" N LEU G 112 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 159 through 164 removed outlier: 3.571A pdb=" N GLY G 159 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'K' and resid 78 through 81 removed outlier: 4.544A pdb=" N ARG K 28 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS K 19 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL K 97 " --> pdb=" O LYS K 19 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG K 21 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR K 95 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU K 23 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL K 97 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR L 84 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 13.153A pdb=" N ASP K 99 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 15.342A pdb=" N LEU L 82 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU L 82 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR L 41 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN L 86 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE L 39 " --> pdb=" O ASN L 86 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE L 39 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR L 28 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL L 43 " --> pdb=" O TRP L 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 26 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU L 45 " --> pdb=" O THR L 24 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR L 24 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL M 84 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS M 79 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN M 86 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR M 77 " --> pdb=" O ASN M 86 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU M 88 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU M 75 " --> pdb=" O GLU M 88 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE M 90 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS M 73 " --> pdb=" O PHE M 90 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER M 92 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU M 69 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS M 59 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN M 71 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG M 57 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE M 55 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL M 103 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU P 70 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU P 58 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY P 66 " --> pdb=" O GLU P 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 78 through 81 removed outlier: 4.544A pdb=" N ARG K 28 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LYS K 19 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL K 97 " --> pdb=" O LYS K 19 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG K 21 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR K 95 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU K 23 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL K 97 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR L 84 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 13.153A pdb=" N ASP K 99 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 15.342A pdb=" N LEU L 82 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU L 82 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR L 41 " --> pdb=" O TYR L 84 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN L 86 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE L 39 " --> pdb=" O ASN L 86 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE L 39 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR L 28 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL L 43 " --> pdb=" O TRP L 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 26 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU L 45 " --> pdb=" O THR L 24 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR L 24 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL M 84 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS M 79 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN M 86 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR M 77 " --> pdb=" O ASN M 86 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU M 88 " --> pdb=" O LEU M 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU M 75 " --> pdb=" O GLU M 88 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE M 90 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS M 73 " --> pdb=" O PHE M 90 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER M 92 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU M 69 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS M 59 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN M 71 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG M 57 " --> pdb=" O ASN M 71 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE M 55 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL M 103 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU P 70 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU P 51 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR P 45 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU P 53 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL P 43 " --> pdb=" O LEU P 53 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU P 55 " --> pdb=" O THR P 41 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR P 41 " --> pdb=" O GLU P 55 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG P 26 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU P 83 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY P 28 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE P 81 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS P 30 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU P 83 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS O 79 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL O 58 " --> pdb=" O PRO O 76 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY O 78 " --> pdb=" O GLU O 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL O 52 " --> pdb=" O PHE O 46 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE O 46 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE O 54 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL O 44 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU O 56 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS O 42 " --> pdb=" O GLU O 56 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE O 37 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU O 31 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU O 89 " --> pdb=" O TRP O 30 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL Q 39 " --> pdb=" O ARG Q 30 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 34 through 36 removed outlier: 6.599A pdb=" N VAL K 44 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE N 71 " --> pdb=" O GLU N 22 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR N 28 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA N 49 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG N 30 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL N 47 " --> pdb=" O ARG N 30 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN N 43 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL N 42 " --> pdb=" O VAL N 64 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP N 60 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE N 48 " --> pdb=" O HIS N 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS N 58 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR N 50 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL N 56 " --> pdb=" O THR N 50 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 106 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4081 1.32 - 1.44: 9454 1.44 - 1.57: 14984 1.57 - 1.69: 650 1.69 - 1.82: 141 Bond restraints: 29310 Sorted by residual: bond pdb=" O3' A R 324 " pdb=" P A R 325 " ideal model delta sigma weight residual 1.607 1.321 0.286 1.50e-02 4.44e+03 3.64e+02 bond pdb=" O3' G R 300 " pdb=" P U R 301 " ideal model delta sigma weight residual 1.607 1.720 -0.113 1.50e-02 4.44e+03 5.70e+01 bond pdb=" C1' U R 301 " pdb=" N1 U R 301 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.05e+01 bond pdb=" O3' G R 35 " pdb=" P U R 36 " ideal model delta sigma weight residual 1.607 1.547 0.060 1.50e-02 4.44e+03 1.58e+01 bond pdb=" O3' A R 323 " pdb=" P A R 324 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.50e-02 4.44e+03 8.84e+00 ... (remaining 29305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.55: 41200 7.55 - 15.10: 36 15.10 - 22.65: 4 22.65 - 30.20: 1 30.20 - 37.74: 1 Bond angle restraints: 41242 Sorted by residual: angle pdb=" O3' A R 324 " pdb=" P A R 325 " pdb=" O5' A R 325 " ideal model delta sigma weight residual 104.00 141.74 -37.74 1.50e+00 4.44e-01 6.33e+02 angle pdb=" O3' G R 300 " pdb=" P U R 301 " pdb=" O5' U R 301 " ideal model delta sigma weight residual 104.00 82.31 21.69 1.50e+00 4.44e-01 2.09e+02 angle pdb=" C3' A R 324 " pdb=" O3' A R 324 " pdb=" P A R 325 " ideal model delta sigma weight residual 120.20 103.29 16.91 1.50e+00 4.44e-01 1.27e+02 angle pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" CD PRO A 60 " ideal model delta sigma weight residual 112.00 96.52 15.48 1.40e+00 5.10e-01 1.22e+02 angle pdb=" O3' U R 301 " pdb=" P U R 302 " pdb=" O5' U R 302 " ideal model delta sigma weight residual 104.00 118.09 -14.09 1.50e+00 4.44e-01 8.82e+01 ... (remaining 41237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 17049 35.93 - 71.86: 1005 71.86 - 107.80: 84 107.80 - 143.73: 5 143.73 - 179.66: 17 Dihedral angle restraints: 18160 sinusoidal: 10074 harmonic: 8086 Sorted by residual: dihedral pdb=" O4' C R 144 " pdb=" C1' C R 144 " pdb=" N1 C R 144 " pdb=" C2 C R 144 " ideal model delta sinusoidal sigma weight residual 200.00 38.34 161.66 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' C R 148 " pdb=" C1' C R 148 " pdb=" N1 C R 148 " pdb=" C2 C R 148 " ideal model delta sinusoidal sigma weight residual 200.00 46.37 153.63 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' U R 146 " pdb=" C1' U R 146 " pdb=" N1 U R 146 " pdb=" C2 U R 146 " ideal model delta sinusoidal sigma weight residual -128.00 50.56 -178.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 18157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4618 0.096 - 0.192: 358 0.192 - 0.288: 20 0.288 - 0.384: 5 0.384 - 0.480: 4 Chirality restraints: 5005 Sorted by residual: chirality pdb=" C3' U R 258 " pdb=" C4' U R 258 " pdb=" O3' U R 258 " pdb=" C2' U R 258 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C3' G R 152 " pdb=" C4' G R 152 " pdb=" O3' G R 152 " pdb=" C2' G R 152 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C3' U R 186 " pdb=" C4' U R 186 " pdb=" O3' U R 186 " pdb=" C2' U R 186 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 5002 not shown) Planarity restraints: 4027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 59 " 0.101 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO A 60 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 28 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO C 29 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G R 271 " -0.051 2.00e-02 2.50e+03 2.27e-02 1.55e+01 pdb=" N9 G R 271 " 0.055 2.00e-02 2.50e+03 pdb=" C8 G R 271 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G R 271 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G R 271 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G R 271 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G R 271 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G R 271 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G R 271 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G R 271 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G R 271 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G R 271 " 0.006 2.00e-02 2.50e+03 ... (remaining 4024 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 5 1.98 - 2.71: 1679 2.71 - 3.44: 39164 3.44 - 4.17: 70113 4.17 - 4.90: 115365 Nonbonded interactions: 226326 Sorted by model distance: nonbonded pdb=" NH2 ARG L 117 " pdb=" OP1 U R 36 " model vdw 1.255 3.120 nonbonded pdb=" O2' U R 16 " pdb=" OP2 C R 168 " model vdw 1.485 3.040 nonbonded pdb=" NZ LYS K 114 " pdb=" OP2 U R 302 " model vdw 1.679 3.120 nonbonded pdb=" NZ LYS K 121 " pdb=" C6 U R 278 " model vdw 1.888 3.420 nonbonded pdb=" CE MET N 92 " pdb=" O4' C R 172 " model vdw 1.958 3.460 ... (remaining 226321 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 24.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.160 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.007 0.286 29310 Z= 0.390 Angle : 0.996 37.744 41242 Z= 0.540 Chirality : 0.054 0.480 5005 Planarity : 0.006 0.140 4027 Dihedral : 20.624 179.660 12888 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.33 % Favored : 95.48 % Rotamer: Outliers : 0.41 % Allowed : 22.61 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2677 helix: 1.43 (0.15), residues: 1292 sheet: -0.95 (0.30), residues: 273 loop : -1.42 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 334 TYR 0.032 0.001 TYR E 296 PHE 0.036 0.001 PHE A 59 TRP 0.038 0.002 TRP E 299 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00717 (29310) covalent geometry : angle 0.99575 (41242) hydrogen bonds : bond 0.15598 ( 1329) hydrogen bonds : angle 6.11270 ( 3708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 294 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: D 195 ASP cc_start: 0.8427 (p0) cc_final: 0.8217 (p0) REVERT: E 375 MET cc_start: 0.8342 (tpp) cc_final: 0.8093 (tpp) REVERT: I 4 MET cc_start: 0.7007 (pmm) cc_final: 0.5933 (ttt) REVERT: M 59 LYS cc_start: 0.8148 (tppt) cc_final: 0.7903 (mmtt) outliers start: 9 outliers final: 3 residues processed: 298 average time/residue: 0.2080 time to fit residues: 96.3034 Evaluate side-chains 276 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 273 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain M residue 19 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 40 ASN A 54 HIS A 66 ASN A 67 HIS B 30 HIS B 80 ASN B 94 GLN B 163 ASN B 170 ASN C 28 ASN D 51 GLN D 72 ASN D 153 GLN D 332 ASN D 393 GLN D 400 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 ASN E 387 GLN E 488 ASN E 506 ASN E 533 ASN F 354 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 GLN K 74 ASN L 21 ASN L 90 ASN L 114 ASN M 51 ASN N 15 GLN N 41 ASN O 15 ASN O 51 ASN O 86 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN P 77 ASN Q 53 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.148063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109105 restraints weight = 50489.843| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.25 r_work: 0.3340 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29310 Z= 0.243 Angle : 0.693 10.248 41242 Z= 0.357 Chirality : 0.043 0.246 5005 Planarity : 0.005 0.064 4027 Dihedral : 20.871 178.316 7994 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 4.82 % Allowed : 18.85 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2677 helix: 1.38 (0.15), residues: 1297 sheet: -0.76 (0.33), residues: 239 loop : -1.51 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 74 TYR 0.023 0.002 TYR L 84 PHE 0.027 0.002 PHE A 59 TRP 0.015 0.002 TRP E 299 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00557 (29310) covalent geometry : angle 0.69266 (41242) hydrogen bonds : bond 0.05555 ( 1329) hydrogen bonds : angle 4.42370 ( 3708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 292 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: B 82 GLU cc_start: 0.7739 (mp0) cc_final: 0.7495 (mp0) REVERT: C 73 MET cc_start: 0.7249 (pmm) cc_final: 0.7014 (pmm) REVERT: C 123 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7524 (ppp) REVERT: D 55 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8202 (tp) REVERT: D 195 ASP cc_start: 0.8365 (p0) cc_final: 0.8002 (t70) REVERT: D 335 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8577 (mp) REVERT: E 293 TRP cc_start: 0.7389 (m-90) cc_final: 0.7123 (m-90) REVERT: E 299 TRP cc_start: 0.8490 (t-100) cc_final: 0.8210 (t-100) REVERT: E 452 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7136 (mpp80) REVERT: G 293 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: H 44 LYS cc_start: 0.8683 (tppt) cc_final: 0.8361 (tptp) REVERT: I 4 MET cc_start: 0.7015 (pmm) cc_final: 0.6184 (mtp) REVERT: K 107 GLU cc_start: 0.8568 (tp30) cc_final: 0.8362 (tp30) REVERT: M 15 ARG cc_start: 0.7383 (tpp-160) cc_final: 0.7084 (tpp-160) REVERT: N 37 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7642 (pt0) REVERT: Q 18 ASN cc_start: 0.8390 (p0) cc_final: 0.8086 (p0) REVERT: Q 72 GLU cc_start: 0.8325 (pm20) cc_final: 0.8004 (pt0) outliers start: 105 outliers final: 59 residues processed: 378 average time/residue: 0.1955 time to fit residues: 115.5477 Evaluate side-chains 325 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 62 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 204 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 18 ASN D 198 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN L 90 ASN P 24 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110558 restraints weight = 50573.546| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.18 r_work: 0.3376 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29310 Z= 0.154 Angle : 0.590 9.751 41242 Z= 0.306 Chirality : 0.040 0.237 5005 Planarity : 0.004 0.062 4027 Dihedral : 20.650 178.817 7990 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 4.50 % Allowed : 19.72 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2677 helix: 1.51 (0.15), residues: 1311 sheet: -0.67 (0.33), residues: 237 loop : -1.42 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 334 TYR 0.029 0.001 TYR C 33 PHE 0.017 0.001 PHE A 59 TRP 0.012 0.001 TRP E 562 HIS 0.009 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00349 (29310) covalent geometry : angle 0.59034 (41242) hydrogen bonds : bond 0.04712 ( 1329) hydrogen bonds : angle 4.14002 ( 3708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 295 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8278 (mmtp) REVERT: B 82 GLU cc_start: 0.7764 (mp0) cc_final: 0.7499 (mp0) REVERT: D 55 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (tp) REVERT: D 195 ASP cc_start: 0.8279 (p0) cc_final: 0.8002 (t70) REVERT: E 293 TRP cc_start: 0.7376 (m-90) cc_final: 0.7146 (m-90) REVERT: E 299 TRP cc_start: 0.8557 (t-100) cc_final: 0.8344 (t-100) REVERT: E 452 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7109 (mpp80) REVERT: G 248 LEU cc_start: 0.8433 (tp) cc_final: 0.8148 (tt) REVERT: G 293 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: I 4 MET cc_start: 0.6984 (pmm) cc_final: 0.6308 (mtp) REVERT: K 73 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6809 (pp) REVERT: K 74 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (p0) REVERT: M 59 LYS cc_start: 0.8238 (tppt) cc_final: 0.7957 (tppt) REVERT: N 37 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7643 (pt0) REVERT: N 90 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7483 (mmt90) REVERT: Q 45 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8143 (tm-30) outliers start: 98 outliers final: 54 residues processed: 370 average time/residue: 0.2026 time to fit residues: 118.1166 Evaluate side-chains 327 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 204 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN D 19 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.146513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107672 restraints weight = 50348.446| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.28 r_work: 0.3313 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29310 Z= 0.261 Angle : 0.668 10.254 41242 Z= 0.344 Chirality : 0.042 0.237 5005 Planarity : 0.005 0.064 4027 Dihedral : 20.602 178.751 7990 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 5.69 % Allowed : 20.05 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2677 helix: 1.40 (0.15), residues: 1310 sheet: -0.98 (0.32), residues: 251 loop : -1.56 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.020 0.002 TYR P 80 PHE 0.022 0.002 PHE M 95 TRP 0.012 0.001 TRP D 186 HIS 0.007 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00611 (29310) covalent geometry : angle 0.66764 (41242) hydrogen bonds : bond 0.05226 ( 1329) hydrogen bonds : angle 4.25365 ( 3708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 280 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: B 3 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6098 (tttt) REVERT: C 86 GLU cc_start: 0.8830 (tp30) cc_final: 0.8422 (mm-30) REVERT: D 66 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: D 195 ASP cc_start: 0.8254 (p0) cc_final: 0.8053 (t70) REVERT: D 335 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 299 TRP cc_start: 0.8624 (t-100) cc_final: 0.8345 (t-100) REVERT: E 452 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7107 (mpp80) REVERT: E 610 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8655 (mmmm) REVERT: G 288 MET cc_start: 0.8123 (tpp) cc_final: 0.7770 (ttp) REVERT: G 293 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: H 3 ASP cc_start: 0.6359 (t0) cc_final: 0.6158 (t0) REVERT: H 44 LYS cc_start: 0.8767 (tptt) cc_final: 0.8468 (tptp) REVERT: I 4 MET cc_start: 0.6877 (pmm) cc_final: 0.6486 (mtp) REVERT: K 73 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6905 (pp) REVERT: K 74 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8059 (p0) REVERT: L 101 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7727 (pt) outliers start: 124 outliers final: 84 residues processed: 380 average time/residue: 0.1992 time to fit residues: 119.2344 Evaluate side-chains 355 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 261 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain E residue 610 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 72 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 6 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 256 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 138 optimal weight: 0.0060 chunk 197 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN K 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110251 restraints weight = 50252.590| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.13 r_work: 0.3380 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29310 Z= 0.136 Angle : 0.573 10.337 41242 Z= 0.296 Chirality : 0.039 0.227 5005 Planarity : 0.004 0.061 4027 Dihedral : 20.485 178.786 7990 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 4.22 % Allowed : 22.06 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2677 helix: 1.64 (0.15), residues: 1312 sheet: -0.85 (0.33), residues: 242 loop : -1.34 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 334 TYR 0.020 0.001 TYR E 296 PHE 0.014 0.001 PHE D 394 TRP 0.011 0.001 TRP E 562 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00304 (29310) covalent geometry : angle 0.57251 (41242) hydrogen bonds : bond 0.04342 ( 1329) hydrogen bonds : angle 4.02648 ( 3708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 292 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: B 82 GLU cc_start: 0.7476 (mp0) cc_final: 0.7207 (mp0) REVERT: C 86 GLU cc_start: 0.8826 (tp30) cc_final: 0.8321 (mm-30) REVERT: C 89 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8559 (ttp80) REVERT: D 195 ASP cc_start: 0.8251 (p0) cc_final: 0.8012 (t70) REVERT: D 335 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8646 (mp) REVERT: E 299 TRP cc_start: 0.8663 (t-100) cc_final: 0.8347 (t-100) REVERT: E 452 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7091 (mpp80) REVERT: G 293 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: H 35 ASP cc_start: 0.8194 (t70) cc_final: 0.7849 (t70) REVERT: I 4 MET cc_start: 0.6842 (pmm) cc_final: 0.6564 (mtp) REVERT: K 73 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6795 (pp) REVERT: K 74 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8042 (p0) REVERT: K 128 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7754 (mt-10) REVERT: L 101 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7689 (pt) REVERT: M 59 LYS cc_start: 0.8096 (tppt) cc_final: 0.7809 (tppt) REVERT: N 37 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7724 (pt0) REVERT: Q 40 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8666 (pp) outliers start: 92 outliers final: 57 residues processed: 363 average time/residue: 0.2030 time to fit residues: 115.0845 Evaluate side-chains 329 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 167 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 50.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 30 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.147763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109152 restraints weight = 50090.365| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.23 r_work: 0.3335 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29310 Z= 0.198 Angle : 0.613 15.121 41242 Z= 0.314 Chirality : 0.040 0.231 5005 Planarity : 0.004 0.061 4027 Dihedral : 20.441 178.001 7988 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 5.78 % Allowed : 21.51 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2677 helix: 1.64 (0.15), residues: 1312 sheet: -0.91 (0.33), residues: 242 loop : -1.38 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 334 TYR 0.019 0.002 TYR L 84 PHE 0.016 0.001 PHE A 59 TRP 0.009 0.001 TRP D 186 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00461 (29310) covalent geometry : angle 0.61274 (41242) hydrogen bonds : bond 0.04604 ( 1329) hydrogen bonds : angle 4.05311 ( 3708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 267 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: B 36 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7529 (t70) REVERT: C 86 GLU cc_start: 0.8956 (tp30) cc_final: 0.8540 (mm-30) REVERT: C 89 ARG cc_start: 0.8905 (ttp80) cc_final: 0.8619 (ttp80) REVERT: D 163 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8050 (ttmp) REVERT: D 195 ASP cc_start: 0.8297 (p0) cc_final: 0.8067 (t70) REVERT: D 335 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8437 (mp) REVERT: E 299 TRP cc_start: 0.8713 (t-100) cc_final: 0.8369 (t-100) REVERT: E 329 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8173 (mtt90) REVERT: E 452 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7107 (mpp80) REVERT: E 610 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8547 (mmmm) REVERT: G 86 MET cc_start: 0.6356 (ttm) cc_final: 0.5995 (tpt) REVERT: G 155 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6586 (mm) REVERT: G 194 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7510 (m) REVERT: G 293 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: H 44 LYS cc_start: 0.8754 (tptp) cc_final: 0.8359 (tptp) REVERT: I 4 MET cc_start: 0.6876 (pmm) cc_final: 0.6630 (mtp) REVERT: K 128 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7766 (mt-10) REVERT: L 101 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7704 (pt) REVERT: M 31 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: N 37 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7759 (pt0) REVERT: O 73 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6988 (tppt) REVERT: P 65 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (m170) REVERT: Q 40 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8710 (pp) outliers start: 126 outliers final: 82 residues processed: 368 average time/residue: 0.1968 time to fit residues: 114.2591 Evaluate side-chains 358 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain E residue 610 LYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 227 CYS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 72 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 163 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 285 optimal weight: 20.0000 chunk 228 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN K 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110292 restraints weight = 49932.443| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.15 r_work: 0.3371 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29310 Z= 0.145 Angle : 0.582 12.103 41242 Z= 0.298 Chirality : 0.039 0.226 5005 Planarity : 0.004 0.060 4027 Dihedral : 20.391 177.722 7988 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 4.91 % Allowed : 22.52 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2677 helix: 1.75 (0.15), residues: 1313 sheet: -0.81 (0.33), residues: 241 loop : -1.31 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 334 TYR 0.018 0.001 TYR C 33 PHE 0.017 0.001 PHE D 455 TRP 0.023 0.001 TRP E 562 HIS 0.004 0.001 HIS N 58 Details of bonding type rmsd covalent geometry : bond 0.00332 (29310) covalent geometry : angle 0.58227 (41242) hydrogen bonds : bond 0.04277 ( 1329) hydrogen bonds : angle 3.97670 ( 3708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 278 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: C 86 GLU cc_start: 0.8976 (tp30) cc_final: 0.8468 (mm-30) REVERT: C 89 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8502 (ttp80) REVERT: D 195 ASP cc_start: 0.8246 (p0) cc_final: 0.8001 (t70) REVERT: D 335 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8500 (mp) REVERT: E 299 TRP cc_start: 0.8704 (t-100) cc_final: 0.8343 (t-100) REVERT: E 325 PHE cc_start: 0.6743 (m-80) cc_final: 0.6502 (m-80) REVERT: E 329 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8056 (mtt90) REVERT: E 452 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7112 (mpp80) REVERT: E 613 GLN cc_start: 0.7816 (mp10) cc_final: 0.7489 (mt0) REVERT: G 155 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6603 (mm) REVERT: H 35 ASP cc_start: 0.8132 (t70) cc_final: 0.7818 (t70) REVERT: H 44 LYS cc_start: 0.8705 (tptp) cc_final: 0.8403 (tptp) REVERT: K 73 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6712 (pp) REVERT: K 128 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7725 (mt-10) REVERT: L 101 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7618 (pt) REVERT: M 59 LYS cc_start: 0.8095 (tppt) cc_final: 0.7789 (tppt) REVERT: N 37 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7716 (pt0) REVERT: N 51 GLU cc_start: 0.7687 (mp0) cc_final: 0.7407 (mp0) REVERT: N 90 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7539 (mmt90) REVERT: O 73 LYS cc_start: 0.7142 (mmmt) cc_final: 0.6815 (tppt) REVERT: P 65 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7269 (m-70) REVERT: Q 40 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8642 (pp) outliers start: 107 outliers final: 77 residues processed: 367 average time/residue: 0.1983 time to fit residues: 114.4497 Evaluate side-chains 350 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 264 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 223 optimal weight: 0.0270 chunk 106 optimal weight: 0.0020 chunk 189 optimal weight: 0.1980 chunk 175 optimal weight: 0.8980 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN B 40 ASN D 91 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN E 387 GLN E 597 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112143 restraints weight = 50243.213| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.12 r_work: 0.3409 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29310 Z= 0.109 Angle : 0.558 10.972 41242 Z= 0.284 Chirality : 0.038 0.260 5005 Planarity : 0.004 0.056 4027 Dihedral : 20.310 177.843 7988 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 3.58 % Allowed : 23.72 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2677 helix: 1.88 (0.15), residues: 1319 sheet: -0.72 (0.32), residues: 250 loop : -1.18 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 334 TYR 0.026 0.001 TYR E 296 PHE 0.014 0.001 PHE D 115 TRP 0.010 0.001 TRP L 26 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00233 (29310) covalent geometry : angle 0.55759 (41242) hydrogen bonds : bond 0.03910 ( 1329) hydrogen bonds : angle 3.85771 ( 3708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 GLU cc_start: 0.9001 (tp30) cc_final: 0.8505 (mm-30) REVERT: C 89 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8475 (ttp80) REVERT: D 195 ASP cc_start: 0.8225 (p0) cc_final: 0.8023 (t70) REVERT: E 299 TRP cc_start: 0.8716 (t-100) cc_final: 0.8359 (t-100) REVERT: E 329 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7994 (mtt90) REVERT: E 375 MET cc_start: 0.8435 (tpp) cc_final: 0.8190 (tpp) REVERT: E 452 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7150 (mpp80) REVERT: E 613 GLN cc_start: 0.7781 (mp10) cc_final: 0.7560 (mt0) REVERT: F 509 MET cc_start: 0.8069 (tmm) cc_final: 0.7851 (tmm) REVERT: G 155 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6574 (mm) REVERT: G 293 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: H 44 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8404 (tptp) REVERT: K 73 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6731 (pp) REVERT: K 118 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8435 (tm-30) REVERT: K 128 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7718 (mt-10) REVERT: M 31 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7596 (mtt) REVERT: M 79 LYS cc_start: 0.7504 (pttm) cc_final: 0.7288 (pttm) REVERT: N 13 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7190 (mm-30) REVERT: N 37 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7659 (pt0) REVERT: N 51 GLU cc_start: 0.7593 (mp0) cc_final: 0.7295 (mp0) REVERT: Q 40 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8557 (pp) REVERT: Q 75 ASP cc_start: 0.7287 (m-30) cc_final: 0.7064 (m-30) outliers start: 78 outliers final: 55 residues processed: 341 average time/residue: 0.1982 time to fit residues: 106.3296 Evaluate side-chains 327 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 297 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 234 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN K 74 ASN ** L 90 ASN ** 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 = 0.4236 r_free = 0.4236 target = 0.148193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108906 restraints weight = 50498.991| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.23 r_work: 0.3348 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29310 Z= 0.181 Angle : 0.615 16.101 41242 Z= 0.312 Chirality : 0.040 0.227 5005 Planarity : 0.004 0.063 4027 Dihedral : 20.289 177.711 7988 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 4.08 % Allowed : 23.39 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2677 helix: 1.82 (0.15), residues: 1303 sheet: -0.80 (0.33), residues: 241 loop : -1.24 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 334 TYR 0.024 0.002 TYR E 296 PHE 0.016 0.001 PHE M 95 TRP 0.014 0.001 TRP E 562 HIS 0.005 0.001 HIS E 573 Details of bonding type rmsd covalent geometry : bond 0.00423 (29310) covalent geometry : angle 0.61492 (41242) hydrogen bonds : bond 0.04355 ( 1329) hydrogen bonds : angle 3.96497 ( 3708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6033 (mtmt) REVERT: B 36 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7684 (t70) REVERT: C 73 MET cc_start: 0.6832 (pmm) cc_final: 0.6613 (pmm) REVERT: C 86 GLU cc_start: 0.9036 (tp30) cc_final: 0.8081 (mm-30) REVERT: C 89 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8193 (ttp80) REVERT: E 299 TRP cc_start: 0.8714 (t-100) cc_final: 0.8331 (t-100) REVERT: E 325 PHE cc_start: 0.6787 (m-80) cc_final: 0.6560 (m-80) REVERT: E 329 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8122 (mtt90) REVERT: E 375 MET cc_start: 0.8529 (tpp) cc_final: 0.8259 (tpp) REVERT: E 452 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7094 (mpp80) REVERT: E 610 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8521 (mmmm) REVERT: E 613 GLN cc_start: 0.7755 (mp10) cc_final: 0.7539 (mt0) REVERT: G 86 MET cc_start: 0.6492 (ttm) cc_final: 0.5829 (mmm) REVERT: G 155 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6647 (mm) REVERT: H 44 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8409 (tptp) REVERT: I 4 MET cc_start: 0.6861 (pmm) cc_final: 0.5519 (ttt) REVERT: K 73 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6821 (pp) REVERT: K 128 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7794 (mt-10) REVERT: M 31 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7771 (mtt) REVERT: M 59 LYS cc_start: 0.8179 (tppt) cc_final: 0.7776 (tptt) REVERT: M 79 LYS cc_start: 0.7600 (pttm) cc_final: 0.7392 (pttm) REVERT: N 37 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7703 (pt0) REVERT: N 51 GLU cc_start: 0.7682 (mp0) cc_final: 0.7383 (mp0) REVERT: Q 40 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8700 (pp) outliers start: 89 outliers final: 69 residues processed: 347 average time/residue: 0.1969 time to fit residues: 107.1976 Evaluate side-chains 340 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 261 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain E residue 610 LYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 251 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.0170 chunk 213 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN K 57 GLN K 74 ASN ** L 90 ASN ** 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 = 0.4241 r_free = 0.4241 target = 0.148421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109664 restraints weight = 49971.836| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.16 r_work: 0.3359 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 29310 Z= 0.176 Angle : 0.714 59.197 41242 Z= 0.382 Chirality : 0.040 0.521 5005 Planarity : 0.004 0.062 4027 Dihedral : 20.291 177.727 7988 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 4.08 % Allowed : 23.67 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2677 helix: 1.82 (0.15), residues: 1303 sheet: -0.79 (0.33), residues: 241 loop : -1.25 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 334 TYR 0.026 0.002 TYR D 183 PHE 0.014 0.001 PHE M 95 TRP 0.011 0.001 TRP E 562 HIS 0.013 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00402 (29310) covalent geometry : angle 0.71393 (41242) hydrogen bonds : bond 0.04331 ( 1329) hydrogen bonds : angle 3.96898 ( 3708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5354 Ramachandran restraints generated. 2677 Oldfield, 0 Emsley, 2677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 265 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7584 (t70) REVERT: C 86 GLU cc_start: 0.9009 (tp30) cc_final: 0.8128 (mm-30) REVERT: C 89 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8193 (ttp80) REVERT: E 299 TRP cc_start: 0.8741 (t-100) cc_final: 0.8361 (t-100) REVERT: E 329 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8075 (mtt90) REVERT: E 452 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7080 (mpp80) REVERT: E 610 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8563 (mmmm) REVERT: G 86 MET cc_start: 0.6426 (ttm) cc_final: 0.5799 (mmm) REVERT: G 155 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6609 (mm) REVERT: G 194 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7530 (m) REVERT: H 44 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8397 (tptp) REVERT: I 4 MET cc_start: 0.6866 (pmm) cc_final: 0.5527 (ttt) REVERT: K 73 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6782 (pp) REVERT: K 128 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7787 (mt-10) REVERT: M 12 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7643 (mm-30) REVERT: M 31 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: M 59 LYS cc_start: 0.8153 (tppt) cc_final: 0.7737 (tptt) REVERT: M 79 LYS cc_start: 0.7611 (pttm) cc_final: 0.7403 (pttm) REVERT: N 13 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7219 (mm-30) REVERT: N 37 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7668 (pt0) REVERT: N 51 GLU cc_start: 0.7656 (mp0) cc_final: 0.7342 (mp0) REVERT: P 65 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: Q 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8679 (pp) outliers start: 89 outliers final: 71 residues processed: 341 average time/residue: 0.1903 time to fit residues: 101.8603 Evaluate side-chains 346 residues out of total 2543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 264 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 329 ARG Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 573 HIS Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain E residue 610 LYS Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 193 ASN Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 206 CYS Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 261 PHE Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 45 HIS Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 31 MET Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 78 GLU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 49 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 34 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 280 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 GLN ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN K 74 ASN ** L 90 ASN ** 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 = 0.4240 r_free = 0.4240 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108864 restraints weight = 50210.652| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.19 r_work: 0.3351 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 29310 Z= 0.176 Angle : 0.714 59.197 41242 Z= 0.382 Chirality : 0.040 0.521 5005 Planarity : 0.004 0.062 4027 Dihedral : 20.291 177.727 7988 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 3.85 % Allowed : 23.90 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2677 helix: 1.82 (0.15), residues: 1303 sheet: -0.79 (0.33), residues: 241 loop : -1.25 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 334 TYR 0.026 0.002 TYR D 183 PHE 0.014 0.001 PHE M 95 TRP 0.011 0.001 TRP E 562 HIS 0.013 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00402 (29310) covalent geometry : angle 0.71393 (41242) hydrogen bonds : bond 0.04331 ( 1329) hydrogen bonds : angle 3.96898 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7308.44 seconds wall clock time: 126 minutes 24.85 seconds (7584.85 seconds total)