Starting phenix.real_space_refine on Wed Mar 20 09:58:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebt_27997/03_2024/8ebt_27997_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 6 6.06 5 P 89 5.49 5 S 157 5.16 5 C 16949 2.51 5 N 4682 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 713": "NH1" <-> "NH2" Residue "H ARG 718": "NH1" <-> "NH2" Residue "H ARG 725": "NH1" <-> "NH2" Residue "H PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 211": "NH1" <-> "NH2" Residue "K ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27026 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4874 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 24, 'TRANS': 578} Chain breaks: 2 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5457 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 29, 'TRANS': 647} Chain breaks: 1 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1547 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3499 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 1 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 361} Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2224 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 Chain: "J" Number of atoms: 573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 558 Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1450 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 930 Unusual residues: {'VM6': 1} Classifications: {'DNA': 43, 'undetermined': 1} Link IDs: {'rna3p': 41, None: 2} Not linked: pdbres=" DT L 29 " pdbres="VM6 L 30 " Not linked: pdbres="VM6 L 30 " pdbres=" DT L 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "M" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 911 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5817 SG CYS B 116 54.366 31.067 50.625 1.00268.67 S ATOM 6126 SG CYS B 155 50.626 27.269 46.607 1.00326.40 S ATOM 5957 SG CYS B 134 52.156 33.156 44.782 1.00320.89 S ATOM 6415 SG CYS B 190 48.172 32.558 49.078 1.00265.74 S ATOM 18044 SG CYS E 345 42.931 60.325 139.758 1.00129.10 S ATOM 18066 SG CYS E 348 44.762 63.560 140.546 1.00125.11 S ATOM 18223 SG CYS E 368 42.938 63.196 137.209 1.00135.96 S ATOM 18244 SG CYS E 371 46.080 61.213 137.874 1.00133.75 S ATOM 18164 SG CYS E 360 41.639 48.885 134.861 1.00139.08 S ATOM 18182 SG CYS E 363 42.326 49.102 138.598 1.00142.19 S ATOM 18331 SG CYS E 382 44.630 50.832 136.215 1.00131.40 S ATOM 18348 SG CYS E 385 44.613 47.026 136.306 1.00137.03 S ATOM 17608 SG CYS E 291 81.228 37.439 129.165 1.00151.40 S ATOM 17630 SG CYS E 294 84.794 36.157 128.700 1.00160.52 S ATOM 17719 SG CYS E 305 83.329 38.463 126.109 1.00159.03 S ATOM 17742 SG CYS E 308 81.959 34.953 126.432 1.00162.98 S ATOM 20244 SG CYS F 268 61.071 35.857 120.706 1.00113.95 S ATOM 20263 SG CYS F 271 58.491 37.806 122.711 1.00115.58 S ATOM 20348 SG CYS F 282 58.619 34.052 123.029 1.00128.26 S ATOM 20368 SG CYS F 285 57.430 35.622 119.764 1.00133.59 S ATOM 20136 SG CYS F 255 62.814 33.187 132.988 1.00130.28 S ATOM 20153 SG CYS F 257 60.260 30.359 133.103 1.00131.84 S ATOM 20302 SG CYS F 276 64.046 29.583 133.502 1.00130.79 S ATOM 23752 SG CYS K 105 43.274 92.886 28.137 1.00249.87 S ATOM 23776 SG CYS K 108 42.636 92.325 24.430 1.00257.08 S ATOM 23924 SG CYS K 126 45.275 90.263 26.211 1.00230.55 S ATOM 23946 SG CYS K 129 45.854 93.947 25.488 1.00226.55 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 15.33, per 1000 atoms: 0.57 Number of scatterers: 27026 At special positions: 0 Unit cell: (153.272, 156.604, 184.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 Ca 2 19.99 S 157 16.00 P 89 15.00 O 5137 8.00 N 4682 7.00 C 16949 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.18 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " Number of angles added : 33 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 24 sheets defined 44.8% alpha, 9.2% beta 40 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 12.76 Creating SS restraints... Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.671A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.595A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.562A pdb=" N VAL A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.926A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.541A pdb=" N PHE A 482 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.847A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.217A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 4.340A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.515A pdb=" N ARG A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.561A pdb=" N ASP A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 682' Processing helix chain 'A' and resid 706 through 716 removed outlier: 3.616A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.975A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 4.639A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 209 through 213 removed outlier: 4.248A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.941A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.959A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.129A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.662A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.619A pdb=" N LEU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 removed outlier: 4.027A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.639A pdb=" N ALA B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.588A pdb=" N GLU B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.741A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.792A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.303A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 710 through 724 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.583A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 515 removed outlier: 4.095A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 521 through 546 removed outlier: 4.140A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 50 through 58 removed outlier: 3.558A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 226 removed outlier: 4.243A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 291 removed outlier: 4.211A pdb=" N SER D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 331 removed outlier: 4.082A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 357 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 385 through 400 removed outlier: 4.147A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 removed outlier: 4.227A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 21 Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.300A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 182 through 191 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 277 removed outlier: 4.272A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.260A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 27 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 removed outlier: 3.586A pdb=" N GLU F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 227 removed outlier: 4.735A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.577A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.616A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 52 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 678 through 680 No H-bonds generated for 'chain 'H' and resid 678 through 680' Processing helix chain 'H' and resid 687 through 692 Processing helix chain 'H' and resid 712 through 720 removed outlier: 3.854A pdb=" N LYS H 716 " --> pdb=" O ASN H 712 " (cutoff:3.500A) Processing helix chain 'H' and resid 722 through 727 removed outlier: 4.266A pdb=" N GLU H 726 " --> pdb=" O GLN H 723 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU H 727 " --> pdb=" O LEU H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 764 through 766 No H-bonds generated for 'chain 'H' and resid 764 through 766' Processing helix chain 'H' and resid 779 through 785 Processing helix chain 'H' and resid 819 through 864 Processing helix chain 'H' and resid 890 through 901 Processing helix chain 'H' and resid 904 through 914 removed outlier: 4.179A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) Processing helix chain 'H' and resid 927 through 933 Processing helix chain 'H' and resid 936 through 938 No H-bonds generated for 'chain 'H' and resid 936 through 938' Processing helix chain 'J' and resid 104 through 113 Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 159 through 167 Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 152 through 156 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 197 through 233 removed outlier: 4.181A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER K 233 " --> pdb=" O ALA K 229 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 5.383A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 171 removed outlier: 3.518A pdb=" N VAL A 268 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.553A pdb=" N CYS A 390 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 688 through 690 removed outlier: 7.736A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 623 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= F, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.793A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= H, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.944A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 249 through 251 removed outlier: 3.840A pdb=" N VAL B 249 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 433 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 432 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 417 " --> pdb=" O HIS B 434 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.262A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 620 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.538A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= M, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.797A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 407 through 409 Processing sheet with id= O, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.806A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE E 171 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE E 199 " --> pdb=" O PHE E 171 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= Q, first strand: chain 'F' and resid 67 through 69 removed outlier: 6.379A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= S, first strand: chain 'H' and resid 695 through 697 Processing sheet with id= T, first strand: chain 'H' and resid 705 through 707 removed outlier: 3.881A pdb=" N LYS H 705 " --> pdb=" O LEU H 732 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 771 through 774 Processing sheet with id= V, first strand: chain 'H' and resid 794 through 799 removed outlier: 6.778A pdb=" N VAL H 807 " --> pdb=" O THR H 795 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE H 797 " --> pdb=" O HIS H 805 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS H 805 " --> pdb=" O PHE H 797 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 138 through 140 Processing sheet with id= X, first strand: chain 'K' and resid 250 through 252 removed outlier: 3.733A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 11771 1.43 - 1.64: 15752 1.64 - 1.86: 234 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 27769 Sorted by residual: bond pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " ideal model delta sigma weight residual 1.556 1.359 0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 1.550 1.375 0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 1.563 1.395 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" OP1 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.512 1.658 -0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" OP2 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.512 1.658 -0.146 2.00e-02 2.50e+03 5.30e+01 ... (remaining 27764 not shown) Histogram of bond angle deviations from ideal: 73.68 - 85.74: 12 85.74 - 97.80: 0 97.80 - 109.86: 3835 109.86 - 121.92: 28300 121.92 - 133.97: 5760 Bond angle restraints: 37907 Sorted by residual: angle pdb=" C5 VM6 L 30 " pdb=" C4 VM6 L 30 " pdb=" N2 VM6 L 30 " ideal model delta sigma weight residual 68.46 125.66 -57.20 3.00e+00 1.11e-01 3.63e+02 angle pdb=" C2 VM6 L 30 " pdb=" C4 VM6 L 30 " pdb=" C5 VM6 L 30 " ideal model delta sigma weight residual 156.44 126.10 30.34 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C6 VM6 L 30 " pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 152.65 130.70 21.95 3.00e+00 1.11e-01 5.35e+01 angle pdb=" C4 VM6 L 30 " pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " ideal model delta sigma weight residual 111.19 130.98 -19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 109.47 125.83 -16.36 3.00e+00 1.11e-01 2.97e+01 ... (remaining 37902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 16154 34.36 - 68.71: 424 68.71 - 103.07: 6 103.07 - 137.42: 3 137.42 - 171.78: 1 Dihedral angle restraints: 16588 sinusoidal: 7424 harmonic: 9164 Sorted by residual: dihedral pdb=" C23 VM6 L 30 " pdb=" C24 VM6 L 30 " pdb=" C25 VM6 L 30 " pdb=" O2 VM6 L 30 " ideal model delta sinusoidal sigma weight residual 163.49 -65.71 -130.80 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C4' DT L 18 " pdb=" C3' DT L 18 " pdb=" O3' DT L 18 " pdb=" P DG L 19 " ideal model delta sinusoidal sigma weight residual -140.00 31.78 -171.78 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA VAL B 5 " pdb=" C VAL B 5 " pdb=" N ASP B 6 " pdb=" CA ASP B 6 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 16585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2661 0.026 - 0.053: 978 0.053 - 0.079: 298 0.079 - 0.105: 202 0.105 - 0.131: 74 Chirality restraints: 4213 Sorted by residual: chirality pdb=" CB VAL C 453 " pdb=" CA VAL C 453 " pdb=" CG1 VAL C 453 " pdb=" CG2 VAL C 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE F 60 " pdb=" N ILE F 60 " pdb=" C ILE F 60 " pdb=" CB ILE F 60 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 4210 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 583 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 354 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT M 26 " -0.016 2.00e-02 2.50e+03 8.34e-03 1.74e+00 pdb=" N1 DT M 26 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DT M 26 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT M 26 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT M 26 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT M 26 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT M 26 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT M 26 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT M 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT M 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 714 2.71 - 3.25: 26649 3.25 - 3.80: 44183 3.80 - 4.35: 55221 4.35 - 4.90: 89342 Nonbonded interactions: 216109 Sorted by model distance: nonbonded pdb=" O LEU E 211 " pdb=" OG1 THR E 215 " model vdw 2.157 2.440 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.170 2.440 nonbonded pdb=" O SER H 711 " pdb=" N ARG H 715 " model vdw 2.173 2.520 nonbonded pdb=" O LEU E 30 " pdb=" OG1 THR E 33 " model vdw 2.211 2.440 nonbonded pdb=" OE1 GLN K 174 " pdb=" N2 DG L 24 " model vdw 2.257 2.520 ... (remaining 216104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 13.520 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 89.830 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.003 0.197 27769 Z= 0.250 Angle : 0.600 57.197 37907 Z= 0.296 Chirality : 0.037 0.131 4213 Planarity : 0.003 0.060 4537 Dihedral : 13.160 171.781 10654 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.21 % Allowed : 5.32 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 3094 helix: 2.23 (0.15), residues: 1416 sheet: 0.56 (0.29), residues: 400 loop : -0.55 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 175 HIS 0.002 0.000 HIS B 613 PHE 0.007 0.001 PHE A 89 TYR 0.010 0.001 TYR E 95 ARG 0.002 0.000 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9149 (pp) REVERT: A 644 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9136 (pp) REVERT: B 1 MET cc_start: 0.8449 (ppp) cc_final: 0.8056 (ppp) REVERT: B 57 MET cc_start: 0.8839 (mmt) cc_final: 0.8589 (mmm) REVERT: B 118 HIS cc_start: 0.6612 (OUTLIER) cc_final: 0.6302 (m-70) REVERT: H 764 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7623 (Cg_endo) REVERT: H 778 ASN cc_start: 0.8158 (m-40) cc_final: 0.7827 (t0) REVERT: H 795 THR cc_start: 0.7841 (m) cc_final: 0.7295 (p) REVERT: H 799 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5445 (p90) REVERT: H 823 THR cc_start: 0.9034 (t) cc_final: 0.8625 (p) REVERT: H 827 ASN cc_start: 0.9117 (t0) cc_final: 0.8800 (m-40) REVERT: H 904 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7722 (t-100) REVERT: J 147 ASP cc_start: 0.8631 (t0) cc_final: 0.8293 (m-30) outliers start: 61 outliers final: 11 residues processed: 252 average time/residue: 0.4480 time to fit residues: 170.7992 Evaluate side-chains 138 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 151 optimal weight: 0.0570 chunk 184 optimal weight: 20.0000 chunk 287 optimal weight: 8.9990 overall best weight: 7.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN C 501 GLN C 509 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 116 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 27769 Z= 0.507 Angle : 0.815 37.575 37907 Z= 0.407 Chirality : 0.044 0.255 4213 Planarity : 0.005 0.056 4537 Dihedral : 16.187 178.240 4427 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.46 % Allowed : 8.00 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 3094 helix: 1.61 (0.14), residues: 1447 sheet: -0.05 (0.27), residues: 423 loop : -0.74 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 511 HIS 0.014 0.002 HIS B 164 PHE 0.023 0.002 PHE H 710 TYR 0.024 0.002 TYR E 219 ARG 0.015 0.001 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 116 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7793 (ptt) cc_final: 0.7518 (ptt) REVERT: B 1 MET cc_start: 0.8335 (ppp) cc_final: 0.8029 (ppp) REVERT: B 25 MET cc_start: 0.9482 (mmm) cc_final: 0.9221 (mmm) REVERT: B 57 MET cc_start: 0.8824 (mmt) cc_final: 0.8612 (mmm) REVERT: B 118 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6743 (m-70) REVERT: B 724 MET cc_start: 0.8587 (tpp) cc_final: 0.8232 (tpp) REVERT: C 493 MET cc_start: 0.9255 (mmm) cc_final: 0.8783 (mmp) REVERT: C 545 MET cc_start: 0.4153 (mtt) cc_final: 0.3346 (ptp) REVERT: H 799 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6369 (p90) REVERT: H 823 THR cc_start: 0.9068 (t) cc_final: 0.8764 (p) REVERT: H 827 ASN cc_start: 0.9054 (t0) cc_final: 0.8771 (m-40) REVERT: H 904 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.7422 (t-100) REVERT: J 147 ASP cc_start: 0.8765 (t0) cc_final: 0.8476 (m-30) REVERT: J 166 MET cc_start: 0.4613 (mmp) cc_final: 0.4379 (mmp) outliers start: 68 outliers final: 30 residues processed: 178 average time/residue: 0.4128 time to fit residues: 117.3061 Evaluate side-chains 139 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 125 LYS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 685 HIS Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 MET Chi-restraints excluded: chain K residue 263 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 288 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27769 Z= 0.196 Angle : 0.582 36.864 37907 Z= 0.285 Chirality : 0.039 0.233 4213 Planarity : 0.003 0.067 4537 Dihedral : 16.163 179.790 4421 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.67 % Allowed : 9.20 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 3094 helix: 1.88 (0.14), residues: 1457 sheet: 0.11 (0.27), residues: 405 loop : -0.69 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 539 HIS 0.009 0.001 HIS E 60 PHE 0.015 0.001 PHE G 33 TYR 0.013 0.001 TYR E 358 ARG 0.004 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9286 (pp) REVERT: A 713 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9236 (tt) REVERT: B 1 MET cc_start: 0.8318 (ppp) cc_final: 0.7994 (ppp) REVERT: B 25 MET cc_start: 0.9438 (mmm) cc_final: 0.9149 (mmm) REVERT: B 57 MET cc_start: 0.8811 (mmt) cc_final: 0.8584 (mmm) REVERT: B 118 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6747 (m-70) REVERT: B 581 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 493 MET cc_start: 0.9334 (mmm) cc_final: 0.8902 (mmp) REVERT: D 185 MET cc_start: 0.9025 (mpp) cc_final: 0.8782 (mpp) REVERT: E 154 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8375 (tm-30) REVERT: H 799 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6219 (p90) REVERT: H 823 THR cc_start: 0.9050 (t) cc_final: 0.8723 (p) REVERT: H 827 ASN cc_start: 0.9055 (t0) cc_final: 0.8756 (m-40) REVERT: J 147 ASP cc_start: 0.8726 (t0) cc_final: 0.8423 (m-30) REVERT: K 178 MET cc_start: 0.8529 (mtm) cc_final: 0.8276 (mmt) REVERT: K 214 MET cc_start: 0.9128 (mtm) cc_final: 0.8897 (tpt) REVERT: K 256 MET cc_start: 0.8291 (tpp) cc_final: 0.7142 (mmm) REVERT: K 273 MET cc_start: 0.5719 (mtm) cc_final: 0.5122 (ptp) outliers start: 46 outliers final: 25 residues processed: 152 average time/residue: 0.4656 time to fit residues: 116.0265 Evaluate side-chains 134 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain F residue 125 LYS Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 9.9990 chunk 216 optimal weight: 0.2980 chunk 149 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 289 optimal weight: 40.0000 chunk 306 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 274 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 459 GLN B 522 ASN ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27769 Z= 0.313 Angle : 0.632 36.221 37907 Z= 0.311 Chirality : 0.040 0.165 4213 Planarity : 0.004 0.055 4537 Dihedral : 16.303 178.022 4421 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.32 % Allowed : 9.31 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 3094 helix: 1.76 (0.14), residues: 1461 sheet: -0.11 (0.27), residues: 399 loop : -0.69 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 175 HIS 0.009 0.001 HIS E 60 PHE 0.017 0.001 PHE B 473 TYR 0.017 0.001 TYR E 358 ARG 0.019 0.001 ARG C 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 105 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9297 (tt) REVERT: B 1 MET cc_start: 0.8385 (ppp) cc_final: 0.8087 (ppp) REVERT: B 25 MET cc_start: 0.9426 (mmm) cc_final: 0.9150 (mmm) REVERT: B 57 MET cc_start: 0.8775 (mmt) cc_final: 0.8570 (mmm) REVERT: B 118 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6526 (m170) REVERT: B 581 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8864 (tt) REVERT: C 528 MET cc_start: 0.9364 (mtm) cc_final: 0.9117 (mpp) REVERT: C 545 MET cc_start: 0.3590 (ptp) cc_final: 0.1981 (ppp) REVERT: D 185 MET cc_start: 0.8995 (mpp) cc_final: 0.8790 (mpp) REVERT: D 228 MET cc_start: 0.7691 (tpt) cc_final: 0.7396 (mmt) REVERT: D 441 MET cc_start: 0.8194 (mmm) cc_final: 0.7858 (mmt) REVERT: E 154 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 229 TRP cc_start: 0.9113 (OUTLIER) cc_final: 0.7651 (t60) REVERT: H 799 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6502 (p90) REVERT: H 823 THR cc_start: 0.9046 (t) cc_final: 0.8732 (p) REVERT: H 827 ASN cc_start: 0.9026 (t0) cc_final: 0.8760 (m-40) REVERT: J 147 ASP cc_start: 0.8788 (t0) cc_final: 0.8513 (m-30) REVERT: K 256 MET cc_start: 0.8296 (tpp) cc_final: 0.7205 (mmm) REVERT: K 273 MET cc_start: 0.5781 (mtm) cc_final: 0.5199 (ptp) outliers start: 64 outliers final: 35 residues processed: 164 average time/residue: 0.3694 time to fit residues: 100.3502 Evaluate side-chains 140 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 228 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 261 optimal weight: 50.0000 chunk 211 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 0.0070 chunk 275 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 ASN C 446 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27769 Z= 0.153 Angle : 0.559 35.963 37907 Z= 0.272 Chirality : 0.039 0.160 4213 Planarity : 0.003 0.066 4537 Dihedral : 16.235 179.153 4421 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.03 % Allowed : 9.85 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 3094 helix: 1.89 (0.14), residues: 1444 sheet: -0.09 (0.27), residues: 412 loop : -0.63 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 175 HIS 0.007 0.001 HIS E 60 PHE 0.017 0.001 PHE C 142 TYR 0.013 0.001 TYR A 534 ARG 0.008 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 102 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6771 (ptt) REVERT: A 713 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9221 (tt) REVERT: B 1 MET cc_start: 0.8442 (ppp) cc_final: 0.8048 (ppp) REVERT: B 25 MET cc_start: 0.9384 (mmm) cc_final: 0.9156 (mmm) REVERT: B 57 MET cc_start: 0.8742 (mmt) cc_final: 0.8533 (mmm) REVERT: B 118 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6490 (m170) REVERT: B 581 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8805 (tt) REVERT: C 465 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: C 493 MET cc_start: 0.9236 (mmm) cc_final: 0.8774 (mmp) REVERT: C 528 MET cc_start: 0.9310 (mtm) cc_final: 0.9068 (mpp) REVERT: C 545 MET cc_start: 0.3759 (ptp) cc_final: 0.2599 (ppp) REVERT: E 154 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8203 (tm-30) REVERT: F 229 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.7478 (t60) REVERT: G 16 MET cc_start: 0.9299 (mmm) cc_final: 0.9027 (mmm) REVERT: H 799 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6488 (p90) REVERT: H 823 THR cc_start: 0.9038 (t) cc_final: 0.8725 (p) REVERT: H 827 ASN cc_start: 0.8998 (t0) cc_final: 0.8731 (m-40) REVERT: H 933 HIS cc_start: 0.8213 (t-90) cc_final: 0.7997 (t-90) REVERT: J 147 ASP cc_start: 0.8780 (t0) cc_final: 0.8515 (m-30) REVERT: K 256 MET cc_start: 0.8353 (tpp) cc_final: 0.7382 (mmm) REVERT: K 273 MET cc_start: 0.5764 (mtm) cc_final: 0.5138 (ptp) outliers start: 56 outliers final: 33 residues processed: 155 average time/residue: 0.3594 time to fit residues: 93.3039 Evaluate side-chains 140 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 125 LYS Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 75 optimal weight: 30.0000 chunk 306 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27769 Z= 0.190 Angle : 0.555 35.620 37907 Z= 0.270 Chirality : 0.038 0.169 4213 Planarity : 0.003 0.055 4537 Dihedral : 16.243 178.701 4421 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.81 % Allowed : 10.11 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 3094 helix: 1.95 (0.14), residues: 1441 sheet: -0.09 (0.27), residues: 414 loop : -0.63 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 175 HIS 0.007 0.001 HIS E 60 PHE 0.019 0.001 PHE B 473 TYR 0.013 0.001 TYR E 358 ARG 0.004 0.000 ARG J 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 101 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6976 (ptt) REVERT: A 713 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9225 (tt) REVERT: B 1 MET cc_start: 0.8473 (ppp) cc_final: 0.8094 (ppp) REVERT: B 25 MET cc_start: 0.9377 (mmm) cc_final: 0.9161 (mmm) REVERT: B 118 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6688 (m-70) REVERT: B 581 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8793 (tt) REVERT: C 441 MET cc_start: 0.7245 (tpp) cc_final: 0.6503 (mmm) REVERT: C 493 MET cc_start: 0.9285 (mmm) cc_final: 0.8881 (mmp) REVERT: C 545 MET cc_start: 0.3917 (ptp) cc_final: 0.2772 (ppp) REVERT: F 229 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.7518 (t60) REVERT: G 16 MET cc_start: 0.9386 (mmm) cc_final: 0.9083 (mmm) REVERT: H 799 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6590 (p90) REVERT: H 823 THR cc_start: 0.9056 (t) cc_final: 0.8751 (p) REVERT: H 827 ASN cc_start: 0.9012 (t0) cc_final: 0.8754 (m-40) REVERT: H 933 HIS cc_start: 0.8242 (t-90) cc_final: 0.8000 (t-90) REVERT: J 147 ASP cc_start: 0.8791 (t0) cc_final: 0.8535 (m-30) REVERT: K 214 MET cc_start: 0.9214 (mtt) cc_final: 0.9011 (tpt) REVERT: K 256 MET cc_start: 0.8327 (tpp) cc_final: 0.7415 (mmm) REVERT: K 273 MET cc_start: 0.5888 (mtm) cc_final: 0.5242 (ptp) outliers start: 50 outliers final: 35 residues processed: 148 average time/residue: 0.3729 time to fit residues: 92.3097 Evaluate side-chains 140 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 99 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 714 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27769 Z= 0.383 Angle : 0.701 35.138 37907 Z= 0.348 Chirality : 0.041 0.198 4213 Planarity : 0.004 0.066 4537 Dihedral : 16.632 173.088 4421 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.25 % Allowed : 10.32 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 3094 helix: 1.46 (0.14), residues: 1468 sheet: -0.32 (0.27), residues: 413 loop : -0.68 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 175 HIS 0.013 0.002 HIS E 60 PHE 0.022 0.002 PHE B 473 TYR 0.019 0.002 TYR E 358 ARG 0.006 0.001 ARG J 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 99 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7164 (ptt) REVERT: A 496 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9386 (mp) REVERT: A 590 MET cc_start: 0.8975 (tpp) cc_final: 0.8734 (tpp) REVERT: B 1 MET cc_start: 0.8552 (ppp) cc_final: 0.8173 (ppp) REVERT: B 25 MET cc_start: 0.9449 (mmm) cc_final: 0.9173 (mmm) REVERT: B 118 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6476 (m-70) REVERT: B 623 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9329 (m) REVERT: B 633 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 441 MET cc_start: 0.7576 (tpp) cc_final: 0.7358 (tpp) REVERT: C 493 MET cc_start: 0.9314 (mmm) cc_final: 0.8955 (mmp) REVERT: C 516 TYR cc_start: 0.9129 (m-10) cc_final: 0.8654 (p90) REVERT: C 545 MET cc_start: 0.4127 (ptp) cc_final: 0.3025 (ppp) REVERT: D 441 MET cc_start: 0.8487 (mmt) cc_final: 0.7896 (mmm) REVERT: F 229 TRP cc_start: 0.9149 (OUTLIER) cc_final: 0.7903 (t60) REVERT: H 827 ASN cc_start: 0.9013 (t0) cc_final: 0.8763 (m-40) REVERT: J 147 ASP cc_start: 0.8740 (t0) cc_final: 0.8477 (m-30) REVERT: K 175 TRP cc_start: 0.5638 (OUTLIER) cc_final: 0.4482 (p90) REVERT: K 256 MET cc_start: 0.8367 (tpp) cc_final: 0.7317 (mmm) REVERT: K 273 MET cc_start: 0.6134 (mtm) cc_final: 0.5582 (ptp) outliers start: 62 outliers final: 42 residues processed: 155 average time/residue: 0.3829 time to fit residues: 99.7345 Evaluate side-chains 148 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 99 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 125 LYS Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 659 ILE Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 0.0020 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS H 712 ASN J 125 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27769 Z= 0.148 Angle : 0.579 34.908 37907 Z= 0.284 Chirality : 0.039 0.150 4213 Planarity : 0.003 0.060 4537 Dihedral : 16.471 178.193 4421 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.59 % Allowed : 11.05 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 3094 helix: 1.62 (0.14), residues: 1462 sheet: -0.26 (0.27), residues: 403 loop : -0.67 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 381 HIS 0.006 0.001 HIS E 60 PHE 0.021 0.001 PHE A 659 TYR 0.014 0.001 TYR A 534 ARG 0.005 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 100 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6808 (ptt) REVERT: A 76 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 514 MET cc_start: 0.9320 (tpt) cc_final: 0.9042 (tpt) REVERT: B 1 MET cc_start: 0.8523 (ppp) cc_final: 0.8197 (ppp) REVERT: B 57 MET cc_start: 0.8618 (mmm) cc_final: 0.8184 (mmm) REVERT: B 118 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6770 (m-70) REVERT: B 581 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 465 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: C 545 MET cc_start: 0.3948 (ptp) cc_final: 0.2852 (ppp) REVERT: D 441 MET cc_start: 0.8417 (mmt) cc_final: 0.8163 (mmm) REVERT: F 229 TRP cc_start: 0.9058 (OUTLIER) cc_final: 0.7643 (t60) REVERT: G 48 GLU cc_start: 0.8909 (pt0) cc_final: 0.8588 (pp20) REVERT: H 827 ASN cc_start: 0.8990 (t0) cc_final: 0.8723 (m-40) REVERT: J 147 ASP cc_start: 0.8810 (t0) cc_final: 0.8560 (m-30) REVERT: K 118 MET cc_start: 0.9093 (mmt) cc_final: 0.8749 (mmt) REVERT: K 175 TRP cc_start: 0.4430 (OUTLIER) cc_final: 0.3780 (p90) REVERT: K 214 MET cc_start: 0.8840 (tpt) cc_final: 0.8529 (mtm) REVERT: K 256 MET cc_start: 0.8405 (tpp) cc_final: 0.7435 (mmm) outliers start: 44 outliers final: 33 residues processed: 139 average time/residue: 0.3707 time to fit residues: 86.3589 Evaluate side-chains 138 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 10.0000 chunk 292 optimal weight: 0.8980 chunk 267 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 223 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 257 optimal weight: 7.9990 chunk 269 optimal weight: 0.6980 chunk 283 optimal weight: 0.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS H 778 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27769 Z= 0.179 Angle : 0.580 34.681 37907 Z= 0.283 Chirality : 0.039 0.210 4213 Planarity : 0.003 0.062 4537 Dihedral : 16.432 177.928 4421 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.63 % Allowed : 11.05 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 3094 helix: 1.67 (0.14), residues: 1462 sheet: -0.22 (0.27), residues: 412 loop : -0.67 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 175 HIS 0.008 0.001 HIS F 248 PHE 0.022 0.001 PHE A 659 TYR 0.013 0.001 TYR E 358 ARG 0.003 0.000 ARG J 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 98 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6844 (ptt) REVERT: A 76 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 496 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9222 (mp) REVERT: A 514 MET cc_start: 0.9347 (tpt) cc_final: 0.9040 (tpt) REVERT: A 590 MET cc_start: 0.8968 (tpp) cc_final: 0.8710 (tpp) REVERT: B 1 MET cc_start: 0.8474 (ppp) cc_final: 0.8170 (ppp) REVERT: B 57 MET cc_start: 0.8631 (mmm) cc_final: 0.8182 (mmm) REVERT: B 118 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6780 (m-70) REVERT: B 386 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7940 (mm) REVERT: B 581 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8883 (tt) REVERT: C 465 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: C 493 MET cc_start: 0.9249 (mmm) cc_final: 0.8806 (mmm) REVERT: C 545 MET cc_start: 0.4076 (ptp) cc_final: 0.2976 (ppp) REVERT: F 229 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.7663 (t60) REVERT: H 827 ASN cc_start: 0.9023 (t0) cc_final: 0.8751 (m-40) REVERT: J 147 ASP cc_start: 0.8805 (t0) cc_final: 0.8550 (m-30) REVERT: K 118 MET cc_start: 0.9097 (mmt) cc_final: 0.8815 (mmt) REVERT: K 175 TRP cc_start: 0.4828 (OUTLIER) cc_final: 0.3987 (p90) REVERT: K 214 MET cc_start: 0.8861 (tpt) cc_final: 0.8575 (mtm) REVERT: K 256 MET cc_start: 0.8404 (tpp) cc_final: 0.7455 (mmm) REVERT: K 273 MET cc_start: 0.6113 (mtm) cc_final: 0.5496 (ptp) outliers start: 45 outliers final: 33 residues processed: 139 average time/residue: 0.3764 time to fit residues: 87.5943 Evaluate side-chains 140 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 209 optimal weight: 0.0470 chunk 315 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS H 644 HIS J 125 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27769 Z= 0.300 Angle : 0.642 34.522 37907 Z= 0.315 Chirality : 0.040 0.390 4213 Planarity : 0.003 0.058 4537 Dihedral : 16.550 175.399 4421 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.81 % Allowed : 10.97 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 3094 helix: 1.65 (0.14), residues: 1471 sheet: -0.27 (0.27), residues: 412 loop : -0.63 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 175 HIS 0.020 0.001 HIS F 248 PHE 0.025 0.002 PHE A 659 TYR 0.022 0.001 TYR F 251 ARG 0.004 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 100 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6974 (ptt) REVERT: A 496 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9182 (mp) REVERT: A 514 MET cc_start: 0.9398 (tpt) cc_final: 0.9105 (tpt) REVERT: A 590 MET cc_start: 0.8981 (tpp) cc_final: 0.8729 (tpp) REVERT: B 1 MET cc_start: 0.8517 (ppp) cc_final: 0.8194 (ppp) REVERT: B 57 MET cc_start: 0.8634 (mmm) cc_final: 0.8180 (mmm) REVERT: B 118 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6803 (m-70) REVERT: B 386 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7936 (mm) REVERT: C 465 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7715 (m-10) REVERT: C 516 TYR cc_start: 0.9062 (m-10) cc_final: 0.8595 (p90) REVERT: C 545 MET cc_start: 0.4079 (ptp) cc_final: 0.2684 (ppp) REVERT: D 441 MET cc_start: 0.8629 (mmm) cc_final: 0.7746 (mmt) REVERT: F 229 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.7837 (t60) REVERT: H 827 ASN cc_start: 0.9016 (t0) cc_final: 0.8762 (m-40) REVERT: J 147 ASP cc_start: 0.8799 (t0) cc_final: 0.8537 (m-30) REVERT: K 118 MET cc_start: 0.9094 (mmt) cc_final: 0.8729 (mmt) REVERT: K 175 TRP cc_start: 0.5387 (OUTLIER) cc_final: 0.4415 (p90) REVERT: K 214 MET cc_start: 0.8937 (tpt) cc_final: 0.8638 (mtm) REVERT: K 256 MET cc_start: 0.8446 (tpp) cc_final: 0.7467 (mmm) REVERT: K 273 MET cc_start: 0.6094 (mtm) cc_final: 0.5507 (ptp) outliers start: 50 outliers final: 36 residues processed: 143 average time/residue: 0.4277 time to fit residues: 102.1753 Evaluate side-chains 142 residues out of total 2762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 258 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 0.0370 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 125 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.044526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029935 restraints weight = 261010.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.030708 restraints weight = 142285.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.031179 restraints weight = 99579.301| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27769 Z= 0.168 Angle : 0.585 34.385 37907 Z= 0.284 Chirality : 0.039 0.146 4213 Planarity : 0.003 0.065 4537 Dihedral : 16.495 177.689 4421 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.56 % Allowed : 11.23 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 3094 helix: 1.69 (0.14), residues: 1456 sheet: -0.20 (0.27), residues: 407 loop : -0.65 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 175 HIS 0.007 0.001 HIS E 60 PHE 0.026 0.001 PHE A 659 TYR 0.013 0.001 TYR E 358 ARG 0.007 0.000 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4556.04 seconds wall clock time: 84 minutes 34.73 seconds (5074.73 seconds total)