Starting phenix.real_space_refine on Thu Apr 11 02:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p28_17359/04_2024/8p28_17359_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 13238 2.51 5 N 3688 2.21 5 O 4039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21141 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5187 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 624} Chain breaks: 3 Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "C" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5186 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 624} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5202 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 626} Chain breaks: 3 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 92 Unusual residues: {' MG': 2, 'DTP': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'DTP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.22, per 1000 atoms: 0.53 Number of scatterers: 21141 At special positions: 0 Unit cell: (106.715, 170.05, 130.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 36 15.00 Mg 4 11.99 O 4039 8.00 N 3688 7.00 C 13238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 416 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.19 Conformation dependent library (CDL) restraints added in 4.1 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 16 sheets defined 46.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.640A pdb=" N ARG A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N MET A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.737A pdb=" N ILE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.694A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 122 through 141 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 198 through 214 removed outlier: 4.038A pdb=" N VAL A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 244 Proline residue: A 230 - end of helix removed outlier: 4.351A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.603A pdb=" N LEU A 276 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU A 277 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N HIS A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.701A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.850A pdb=" N ALA A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.904A pdb=" N CYS A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 485 removed outlier: 3.725A pdb=" N ILE A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.967A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 621 through 631 Proline residue: A 630 - end of helix Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.967A pdb=" N VAL A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.520A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 removed outlier: 3.921A pdb=" N GLN B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.698A pdb=" N ILE B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 122 through 141 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.687A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 224 through 231 removed outlier: 4.067A pdb=" N LEU B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.603A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.889A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 409 Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.525A pdb=" N GLY B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 485 removed outlier: 3.532A pdb=" N ASP B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 545 through 569 removed outlier: 3.877A pdb=" N GLU B 549 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.620A pdb=" N GLN B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 634 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.991A pdb=" N GLU B 657 " --> pdb=" O PRO B 653 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.517A pdb=" N ALA C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.606A pdb=" N MET C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 92 removed outlier: 3.949A pdb=" N LYS C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 122 through 141 removed outlier: 3.580A pdb=" N ALA C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 198 through 214 removed outlier: 3.915A pdb=" N ASN C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 236 through 246 removed outlier: 3.712A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 303 removed outlier: 3.748A pdb=" N ASN C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS C 303 " --> pdb=" O MET C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 removed outlier: 4.351A pdb=" N CYS C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 Processing helix chain 'C' and resid 406 through 409 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.766A pdb=" N MET C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 485 removed outlier: 3.681A pdb=" N PHE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 529 through 537 Processing helix chain 'C' and resid 545 through 569 removed outlier: 3.641A pdb=" N GLU C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 552 " --> pdb=" O GLN C 548 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 595 removed outlier: 3.852A pdb=" N LYS C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 627 Processing helix chain 'C' and resid 653 through 665 removed outlier: 3.511A pdb=" N ASP C 664 " --> pdb=" O VAL C 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 removed outlier: 3.959A pdb=" N ALA D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 48 removed outlier: 4.118A pdb=" N GLN D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.897A pdb=" N LYS D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 91 removed outlier: 3.611A pdb=" N GLN D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.629A pdb=" N ILE D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 102' Processing helix chain 'D' and resid 122 through 141 Proline residue: D 136 - end of helix Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'D' and resid 197 through 200 No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 202 through 214 removed outlier: 4.023A pdb=" N SER D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.927A pdb=" N LEU D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 4.185A pdb=" N ARG D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 278 through 304 removed outlier: 4.073A pdb=" N SER D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 removed outlier: 3.580A pdb=" N CYS D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 Processing helix chain 'D' and resid 406 through 409 Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 456 through 485 removed outlier: 3.674A pdb=" N ASP D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 545 through 569 removed outlier: 3.730A pdb=" N LEU D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 552 " --> pdb=" O GLN D 548 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.689A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 634 Proline residue: D 630 - end of helix removed outlier: 4.472A pdb=" N ASP D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU D 634 " --> pdb=" O PRO D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 665 removed outlier: 4.014A pdb=" N GLU D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.701A pdb=" N MET A 55 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 6 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.566A pdb=" N SER A 439 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.340A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.088A pdb=" N SER A 672 " --> pdb=" O VAL A 643 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.512A pdb=" N THR B 521 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY B 523 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 438 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY B 525 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 440 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B 527 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN B 442 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 184 through 186 Processing sheet with id= H, first strand: chain 'B' and resid 314 through 317 removed outlier: 6.552A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 156 through 158 removed outlier: 7.854A pdb=" N THR C 521 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE C 438 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY C 523 " --> pdb=" O PHE C 438 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR C 440 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY C 525 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 526 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.445A pdb=" N ILE C 350 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR C 317 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 352 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN C 385 " --> pdb=" O TRP C 353 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS C 355 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 387 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.825A pdb=" N SER C 672 " --> pdb=" O VAL C 643 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= N, first strand: chain 'D' and resid 156 through 158 removed outlier: 3.743A pdb=" N PHE D 526 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 184 through 186 Processing sheet with id= P, first strand: chain 'D' and resid 314 through 317 removed outlier: 6.417A pdb=" N ILE D 350 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYR D 317 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE D 352 " --> pdb=" O TYR D 317 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN D 385 " --> pdb=" O TRP D 353 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS D 355 " --> pdb=" O ASN D 385 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 387 " --> pdb=" O LYS D 355 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 693 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6944 1.34 - 1.47: 4998 1.47 - 1.60: 9395 1.60 - 1.73: 0 1.73 - 1.85: 236 Bond restraints: 21573 Sorted by residual: bond pdb=" N VAL A 377 " pdb=" CA VAL A 377 " ideal model delta sigma weight residual 1.462 1.508 -0.046 1.18e-02 7.18e+03 1.49e+01 bond pdb=" N VAL C 502 " pdb=" CA VAL C 502 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.27e-02 6.20e+03 1.03e+01 bond pdb=" N THR B 588 " pdb=" CA THR B 588 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.85e+00 ... (remaining 21568 not shown) Histogram of bond angle deviations from ideal: 98.71 - 106.97: 727 106.97 - 115.22: 12960 115.22 - 123.47: 14768 123.47 - 131.72: 641 131.72 - 139.97: 57 Bond angle restraints: 29153 Sorted by residual: angle pdb=" CA PHE C 184 " pdb=" CB PHE C 184 " pdb=" CG PHE C 184 " ideal model delta sigma weight residual 113.80 118.62 -4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" N GLN A 334 " pdb=" CA GLN A 334 " pdb=" C GLN A 334 " ideal model delta sigma weight residual 113.55 107.79 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" CA ASN A 385 " pdb=" C ASN A 385 " pdb=" O ASN A 385 " ideal model delta sigma weight residual 121.88 116.99 4.89 1.13e+00 7.83e-01 1.87e+01 angle pdb=" N PRO C 175 " pdb=" CA PRO C 175 " pdb=" C PRO C 175 " ideal model delta sigma weight residual 112.47 104.01 8.46 2.06e+00 2.36e-01 1.69e+01 angle pdb=" CA TRP C 501 " pdb=" C TRP C 501 " pdb=" O TRP C 501 " ideal model delta sigma weight residual 121.25 116.86 4.39 1.09e+00 8.42e-01 1.62e+01 ... (remaining 29148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.33: 12402 20.33 - 40.66: 607 40.66 - 60.99: 131 60.99 - 81.32: 54 81.32 - 101.65: 10 Dihedral angle restraints: 13204 sinusoidal: 5660 harmonic: 7544 Sorted by residual: dihedral pdb=" CA TYR B 606 " pdb=" C TYR B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER D 71 " pdb=" C SER D 71 " pdb=" N ALA D 72 " pdb=" CA ALA D 72 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASP A 603 " pdb=" C ASP A 603 " pdb=" N ARG A 604 " pdb=" CA ARG A 604 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 13201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2517 0.054 - 0.108: 477 0.108 - 0.161: 106 0.161 - 0.215: 3 0.215 - 0.269: 25 Chirality restraints: 3128 Sorted by residual: chirality pdb=" C4' DTP A 802 " pdb=" C3' DTP A 802 " pdb=" C5' DTP A 802 " pdb=" O4' DTP A 802 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU C 505 " pdb=" N GLU C 505 " pdb=" C GLU C 505 " pdb=" CB GLU C 505 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' DTP D 801 " pdb=" C2' DTP D 801 " pdb=" C4' DTP D 801 " pdb=" O3' DTP D 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.94 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3125 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 604 " 0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG B 604 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 604 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 604 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 604 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 182 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C HIS C 182 " 0.043 2.00e-02 2.50e+03 pdb=" O HIS C 182 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY C 183 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 173 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLN C 173 " 0.036 2.00e-02 2.50e+03 pdb=" O GLN C 173 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS C 174 " -0.012 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 84 2.42 - 3.04: 13911 3.04 - 3.66: 28892 3.66 - 4.28: 44873 4.28 - 4.90: 76674 Nonbonded interactions: 164434 Sorted by model distance: nonbonded pdb=" O3A DTP C 801 " pdb="MG MG C 804 " model vdw 1.795 2.170 nonbonded pdb=" O2B DTP A 801 " pdb="MG MG B 804 " model vdw 1.817 2.170 nonbonded pdb="MG MG A 804 " pdb=" O2B DTP B 801 " model vdw 1.842 2.170 nonbonded pdb=" OE2 GLU C 293 " pdb="MG MG C 805 " model vdw 1.859 2.170 nonbonded pdb="MG MG C 805 " pdb=" O2B DTP D 801 " model vdw 1.876 2.170 ... (remaining 164429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) selection = (chain 'B' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) selection = (chain 'C' and (resid 1 through 674 or resid 801 through 803)) selection = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 120 through 674 or resid 801 through 803)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 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: 21.910 Check model and map are aligned: 0.090 Set scattering table: 0.180 Process input model: 58.890 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21573 Z= 0.347 Angle : 0.641 8.461 29153 Z= 0.378 Chirality : 0.049 0.269 3128 Planarity : 0.005 0.144 3712 Dihedral : 13.734 101.650 8345 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.99 % Favored : 89.81 % Rotamer: Outliers : 2.15 % Allowed : 7.02 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -1.36 (0.17), residues: 2552 helix: 0.39 (0.16), residues: 1162 sheet: 0.03 (0.37), residues: 250 loop : -2.60 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 353 HIS 0.006 0.001 HIS A 289 PHE 0.020 0.002 PHE B 184 TYR 0.021 0.002 TYR A 262 ARG 0.004 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 567 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8205 (tp) cc_final: 0.7900 (tt) REVERT: A 154 ASN cc_start: 0.8141 (t0) cc_final: 0.7869 (t0) REVERT: A 468 ASP cc_start: 0.6788 (t0) cc_final: 0.6525 (t0) REVERT: A 533 LEU cc_start: 0.8020 (mp) cc_final: 0.7749 (mp) REVERT: A 670 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.8101 (t80) REVERT: B 41 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 160 ASP cc_start: 0.7102 (t70) cc_final: 0.6824 (t70) REVERT: B 296 ILE cc_start: 0.6872 (mt) cc_final: 0.6661 (mp) REVERT: B 369 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.6721 (p0) REVERT: B 388 ASN cc_start: 0.7784 (t0) cc_final: 0.7451 (t0) REVERT: B 446 LEU cc_start: 0.8332 (mt) cc_final: 0.8118 (mt) REVERT: B 449 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 521 THR cc_start: 0.7680 (p) cc_final: 0.7449 (m) REVERT: B 560 ASP cc_start: 0.7995 (m-30) cc_final: 0.7646 (m-30) REVERT: B 665 LYS cc_start: 0.8649 (tppp) cc_final: 0.8286 (mtpp) REVERT: C 2 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 41 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6673 (mt-10) REVERT: C 45 ASP cc_start: 0.7098 (m-30) cc_final: 0.6805 (m-30) REVERT: C 65 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 67 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 79 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6784 (mttt) REVERT: C 188 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8044 (p-80) REVERT: C 344 GLU cc_start: 0.6884 (pm20) cc_final: 0.6528 (pm20) REVERT: C 454 GLU cc_start: 0.7263 (tm-30) cc_final: 0.7021 (tm-30) REVERT: D 29 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (tt) REVERT: D 192 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6970 (ptt90) REVERT: D 369 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.7444 (p0) REVERT: D 420 VAL cc_start: 0.8428 (p) cc_final: 0.8221 (p) REVERT: D 560 ASP cc_start: 0.8018 (m-30) cc_final: 0.7789 (m-30) outliers start: 48 outliers final: 10 residues processed: 601 average time/residue: 1.3841 time to fit residues: 940.5637 Evaluate side-chains 528 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 511 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 494 PRO Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.0570 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN A 455 ASN A 477 GLN B 279 HIS B 385 ASN B 396 ASN C 30 HIS C 213 ASN C 667 ASN D 442 ASN D 572 ASN D 639 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21573 Z= 0.243 Angle : 0.607 12.557 29153 Z= 0.316 Chirality : 0.044 0.191 3128 Planarity : 0.004 0.053 3712 Dihedral : 12.186 94.204 3227 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.53 % Allowed : 15.12 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -1.11 (0.17), residues: 2552 helix: 0.60 (0.16), residues: 1172 sheet: -0.02 (0.36), residues: 254 loop : -2.44 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 425 HIS 0.010 0.001 HIS D 297 PHE 0.026 0.002 PHE B 526 TYR 0.015 0.001 TYR A 236 ARG 0.006 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 525 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 60 ILE cc_start: 0.8115 (tp) cc_final: 0.7798 (tt) REVERT: A 154 ASN cc_start: 0.8079 (t0) cc_final: 0.7826 (t0) REVERT: A 468 ASP cc_start: 0.6683 (t0) cc_final: 0.6346 (t70) REVERT: B 41 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6526 (mm-30) REVERT: B 152 MET cc_start: 0.6486 (mtm) cc_final: 0.6198 (mtm) REVERT: B 160 ASP cc_start: 0.7154 (t70) cc_final: 0.6860 (t70) REVERT: B 296 ILE cc_start: 0.6896 (mt) cc_final: 0.6653 (mp) REVERT: B 369 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.6502 (p0) REVERT: B 420 VAL cc_start: 0.8141 (p) cc_final: 0.7910 (m) REVERT: B 449 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 560 ASP cc_start: 0.8053 (m-30) cc_final: 0.7846 (m-30) REVERT: B 631 TYR cc_start: 0.7773 (m-80) cc_final: 0.7376 (m-80) REVERT: B 665 LYS cc_start: 0.8601 (tppp) cc_final: 0.8245 (mtpp) REVERT: C 2 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7395 (mp) REVERT: C 41 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6623 (mt-10) REVERT: C 45 ASP cc_start: 0.7019 (m-30) cc_final: 0.6751 (m-30) REVERT: C 52 LYS cc_start: 0.7651 (mmmm) cc_final: 0.7297 (mmmm) REVERT: C 67 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 75 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6398 (p0) REVERT: C 79 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6955 (mttt) REVERT: C 154 ASN cc_start: 0.8362 (t0) cc_final: 0.7872 (t0) REVERT: C 178 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8257 (m) REVERT: C 208 LEU cc_start: 0.7367 (mp) cc_final: 0.7028 (mp) REVERT: C 225 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6215 (p0) REVERT: C 344 GLU cc_start: 0.7011 (pm20) cc_final: 0.6653 (pm20) REVERT: C 454 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6987 (tm-30) REVERT: C 592 ARG cc_start: 0.7637 (ttp-170) cc_final: 0.7311 (ttm170) REVERT: D 41 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6589 (mm-30) REVERT: D 185 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8289 (p) REVERT: D 311 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7773 (t) REVERT: D 369 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.6981 (p0) REVERT: D 420 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8155 (p) REVERT: D 468 ASP cc_start: 0.5752 (OUTLIER) cc_final: 0.5405 (t70) outliers start: 79 outliers final: 28 residues processed: 565 average time/residue: 1.4303 time to fit residues: 913.3124 Evaluate side-chains 542 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 503 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 213 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 667 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 385 ASN B 396 ASN B 540 HIS C 30 HIS C 154 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 639 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21573 Z= 0.356 Angle : 0.636 13.709 29153 Z= 0.334 Chirality : 0.046 0.211 3128 Planarity : 0.005 0.063 3712 Dihedral : 11.989 92.325 3213 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.88 % Allowed : 16.02 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -1.23 (0.17), residues: 2552 helix: 0.49 (0.16), residues: 1160 sheet: -0.04 (0.36), residues: 256 loop : -2.49 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 425 HIS 0.009 0.001 HIS D 297 PHE 0.028 0.002 PHE B 526 TYR 0.020 0.002 TYR A 164 ARG 0.009 0.001 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 515 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 18 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: A 60 ILE cc_start: 0.8079 (tp) cc_final: 0.7754 (tt) REVERT: A 149 ASP cc_start: 0.7672 (m-30) cc_final: 0.7465 (m-30) REVERT: A 275 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5233 (ttm170) REVERT: A 301 THR cc_start: 0.7780 (t) cc_final: 0.7559 (m) REVERT: A 468 ASP cc_start: 0.6756 (t0) cc_final: 0.6421 (t70) REVERT: B 41 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6595 (mm-30) REVERT: B 160 ASP cc_start: 0.7194 (t70) cc_final: 0.6880 (t70) REVERT: B 185 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 369 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.6751 (p0) REVERT: B 387 LEU cc_start: 0.8231 (tp) cc_final: 0.7974 (tp) REVERT: B 420 VAL cc_start: 0.8224 (p) cc_final: 0.8010 (p) REVERT: B 449 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6900 (tm-30) REVERT: B 560 ASP cc_start: 0.8051 (m-30) cc_final: 0.7841 (m-30) REVERT: C 2 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7425 (mp) REVERT: C 41 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6618 (mt-10) REVERT: C 45 ASP cc_start: 0.7075 (m-30) cc_final: 0.6799 (m-30) REVERT: C 52 LYS cc_start: 0.7646 (mmmm) cc_final: 0.7291 (mmmm) REVERT: C 65 GLU cc_start: 0.7502 (tt0) cc_final: 0.7276 (mt-10) REVERT: C 67 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 75 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6506 (p0) REVERT: C 79 LYS cc_start: 0.7333 (mmtt) cc_final: 0.6960 (mttt) REVERT: C 178 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (m) REVERT: C 225 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6244 (p0) REVERT: C 344 GLU cc_start: 0.7014 (pm20) cc_final: 0.6609 (pm20) REVERT: C 454 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7002 (tm-30) REVERT: C 644 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6534 (mm-30) REVERT: D 35 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5709 (tp30) REVERT: D 41 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6579 (mm-30) REVERT: D 127 MET cc_start: 0.7269 (mmm) cc_final: 0.6962 (mmt) REVERT: D 160 ASP cc_start: 0.6702 (p0) cc_final: 0.6429 (p0) REVERT: D 185 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8261 (p) REVERT: D 188 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7782 (p-80) REVERT: D 369 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.7277 (p0) REVERT: D 420 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8159 (p) outliers start: 109 outliers final: 45 residues processed: 570 average time/residue: 1.2257 time to fit residues: 789.9661 Evaluate side-chains 563 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 504 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 567 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 658 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.0020 chunk 175 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 0.0770 chunk 221 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN A 282 ASN A 351 GLN A 455 ASN A 518 ASN A 667 ASN B 16 ASN B 342 ASN B 385 ASN B 540 HIS C 30 HIS ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21573 Z= 0.179 Angle : 0.562 14.509 29153 Z= 0.292 Chirality : 0.042 0.153 3128 Planarity : 0.004 0.054 3712 Dihedral : 10.948 86.555 3213 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.16 % Allowed : 18.21 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.86 (0.17), residues: 2552 helix: 0.77 (0.16), residues: 1172 sheet: 0.06 (0.36), residues: 258 loop : -2.27 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 425 HIS 0.018 0.001 HIS B 540 PHE 0.032 0.002 PHE B 526 TYR 0.013 0.001 TYR D 670 ARG 0.009 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 515 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 18 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: A 32 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7107 (p0) REVERT: A 60 ILE cc_start: 0.8053 (tp) cc_final: 0.7728 (tt) REVERT: A 149 ASP cc_start: 0.7666 (m-30) cc_final: 0.7420 (m-30) REVERT: A 301 THR cc_start: 0.7843 (t) cc_final: 0.7615 (m) REVERT: A 507 LEU cc_start: 0.8766 (mt) cc_final: 0.8541 (mp) REVERT: B 160 ASP cc_start: 0.7175 (t70) cc_final: 0.6871 (t70) REVERT: B 185 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 369 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.6474 (p0) REVERT: B 420 VAL cc_start: 0.8215 (p) cc_final: 0.7917 (m) REVERT: B 449 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6885 (tm-30) REVERT: B 560 ASP cc_start: 0.8095 (m-30) cc_final: 0.7854 (m-30) REVERT: C 41 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 45 ASP cc_start: 0.6983 (m-30) cc_final: 0.6708 (m-30) REVERT: C 65 GLU cc_start: 0.7487 (tt0) cc_final: 0.7228 (mt-10) REVERT: C 75 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6331 (p0) REVERT: C 76 VAL cc_start: 0.6608 (t) cc_final: 0.6406 (m) REVERT: C 79 LYS cc_start: 0.7237 (mmtt) cc_final: 0.6938 (mttt) REVERT: C 88 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: C 178 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8258 (m) REVERT: C 208 LEU cc_start: 0.7196 (mp) cc_final: 0.6975 (mp) REVERT: C 225 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.6191 (p0) REVERT: C 344 GLU cc_start: 0.7091 (pm20) cc_final: 0.6741 (pm20) REVERT: C 454 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6975 (tm-30) REVERT: D 35 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: D 127 MET cc_start: 0.7221 (mmm) cc_final: 0.6907 (mmt) REVERT: D 160 ASP cc_start: 0.6678 (p0) cc_final: 0.6374 (p0) REVERT: D 185 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8280 (p) REVERT: D 188 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7741 (p-80) REVERT: D 369 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.6974 (p0) REVERT: D 468 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5256 (t70) REVERT: D 491 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7969 (ptmm) outliers start: 93 outliers final: 35 residues processed: 562 average time/residue: 1.3905 time to fit residues: 880.3129 Evaluate side-chains 553 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 503 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.0050 chunk 211 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN A 351 GLN A 455 ASN A 667 ASN B 16 ASN B 342 ASN B 385 ASN B 540 HIS C 30 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21573 Z= 0.192 Angle : 0.555 15.620 29153 Z= 0.288 Chirality : 0.042 0.161 3128 Planarity : 0.004 0.052 3712 Dihedral : 10.372 85.937 3205 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.71 % Allowed : 19.28 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2552 helix: 0.87 (0.16), residues: 1174 sheet: 0.12 (0.36), residues: 258 loop : -2.17 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 425 HIS 0.004 0.001 HIS D 297 PHE 0.032 0.002 PHE B 526 TYR 0.013 0.001 TYR D 670 ARG 0.009 0.000 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 514 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 60 ILE cc_start: 0.8033 (tp) cc_final: 0.7718 (tt) REVERT: A 79 LYS cc_start: 0.7526 (ptpp) cc_final: 0.7322 (ptmt) REVERT: A 215 MET cc_start: 0.8474 (mtm) cc_final: 0.8263 (mtt) REVERT: A 301 THR cc_start: 0.7882 (t) cc_final: 0.7655 (m) REVERT: A 507 LEU cc_start: 0.8699 (mt) cc_final: 0.8489 (mp) REVERT: A 606 TYR cc_start: 0.6971 (p90) cc_final: 0.6662 (p90) REVERT: B 160 ASP cc_start: 0.7192 (t70) cc_final: 0.6876 (t70) REVERT: B 185 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 369 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.6358 (p0) REVERT: B 420 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (m) REVERT: B 446 LEU cc_start: 0.8207 (mt) cc_final: 0.7899 (mt) REVERT: B 449 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6880 (tm-30) REVERT: B 560 ASP cc_start: 0.8096 (m-30) cc_final: 0.7829 (m-30) REVERT: B 631 TYR cc_start: 0.7616 (m-80) cc_final: 0.7206 (m-80) REVERT: C 41 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6587 (mt-10) REVERT: C 45 ASP cc_start: 0.7011 (m-30) cc_final: 0.6747 (m-30) REVERT: C 65 GLU cc_start: 0.7455 (tt0) cc_final: 0.7201 (mt-10) REVERT: C 75 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6274 (p0) REVERT: C 79 LYS cc_start: 0.7248 (mmtt) cc_final: 0.6927 (mttt) REVERT: C 225 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.6195 (p0) REVERT: C 344 GLU cc_start: 0.7096 (pm20) cc_final: 0.6720 (pm20) REVERT: C 454 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 527 ILE cc_start: 0.8428 (tt) cc_final: 0.8203 (pt) REVERT: D 127 MET cc_start: 0.7215 (mmm) cc_final: 0.6716 (mmt) REVERT: D 160 ASP cc_start: 0.6647 (p0) cc_final: 0.6368 (p0) REVERT: D 185 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8274 (p) REVERT: D 188 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7760 (p-80) REVERT: D 192 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7078 (mtt90) REVERT: D 369 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.6991 (p0) REVERT: D 420 VAL cc_start: 0.8237 (p) cc_final: 0.7969 (m) outliers start: 83 outliers final: 37 residues processed: 557 average time/residue: 1.3951 time to fit residues: 876.1761 Evaluate side-chains 550 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 503 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 247 optimal weight: 0.7980 chunk 205 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 88 ASN A 154 ASN A 213 ASN A 351 GLN A 388 ASN A 667 ASN B 16 ASN B 88 ASN B 342 ASN B 385 ASN B 395 GLN B 396 ASN B 540 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 394 ASN D 540 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21573 Z= 0.195 Angle : 0.557 16.615 29153 Z= 0.289 Chirality : 0.043 0.153 3128 Planarity : 0.004 0.052 3712 Dihedral : 10.065 87.415 3204 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.80 % Allowed : 19.87 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.64 (0.17), residues: 2552 helix: 0.91 (0.16), residues: 1180 sheet: 0.24 (0.35), residues: 256 loop : -2.14 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 425 HIS 0.004 0.001 HIS A 289 PHE 0.034 0.002 PHE B 526 TYR 0.012 0.001 TYR D 670 ARG 0.010 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 511 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 60 ILE cc_start: 0.8025 (tp) cc_final: 0.7719 (tt) REVERT: A 215 MET cc_start: 0.8480 (mtm) cc_final: 0.8257 (mtt) REVERT: A 301 THR cc_start: 0.7905 (t) cc_final: 0.7664 (m) REVERT: A 606 TYR cc_start: 0.6957 (p90) cc_final: 0.6656 (p90) REVERT: B 149 ASP cc_start: 0.6987 (t0) cc_final: 0.6774 (t0) REVERT: B 160 ASP cc_start: 0.7204 (t70) cc_final: 0.6885 (t70) REVERT: B 185 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 215 MET cc_start: 0.7406 (mtp) cc_final: 0.6696 (mtm) REVERT: B 369 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.6292 (p0) REVERT: B 420 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 449 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6879 (tm-30) REVERT: B 560 ASP cc_start: 0.8085 (m-30) cc_final: 0.7808 (m-30) REVERT: B 631 TYR cc_start: 0.7540 (m-80) cc_final: 0.7147 (m-80) REVERT: C 41 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6572 (mt-10) REVERT: C 45 ASP cc_start: 0.7020 (m-30) cc_final: 0.6745 (m-30) REVERT: C 65 GLU cc_start: 0.7488 (tt0) cc_final: 0.7255 (tt0) REVERT: C 75 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6323 (p0) REVERT: C 79 LYS cc_start: 0.7252 (mmtt) cc_final: 0.6941 (mttt) REVERT: C 344 GLU cc_start: 0.7107 (pm20) cc_final: 0.6703 (pm20) REVERT: C 454 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 522 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7169 (mp) REVERT: D 185 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8270 (p) REVERT: D 188 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7694 (p-80) REVERT: D 369 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.7022 (p0) REVERT: D 420 VAL cc_start: 0.8284 (p) cc_final: 0.7993 (m) REVERT: D 468 ASP cc_start: 0.5542 (OUTLIER) cc_final: 0.5277 (t70) outliers start: 85 outliers final: 43 residues processed: 556 average time/residue: 1.3852 time to fit residues: 871.0214 Evaluate side-chains 554 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 501 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 138 optimal weight: 0.0070 chunk 246 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 667 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 385 ASN B 395 GLN B 540 HIS ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21573 Z= 0.288 Angle : 0.605 16.995 29153 Z= 0.314 Chirality : 0.045 0.172 3128 Planarity : 0.004 0.057 3712 Dihedral : 10.257 87.144 3200 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.55 % Rotamer: Outliers : 4.03 % Allowed : 20.22 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.73 (0.17), residues: 2552 helix: 0.85 (0.16), residues: 1164 sheet: 0.18 (0.35), residues: 256 loop : -2.14 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 425 HIS 0.006 0.001 HIS A 289 PHE 0.036 0.002 PHE A 383 TYR 0.017 0.002 TYR C 164 ARG 0.011 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 518 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6422 (mpp) REVERT: A 60 ILE cc_start: 0.8029 (tp) cc_final: 0.7725 (tt) REVERT: A 301 THR cc_start: 0.7943 (t) cc_final: 0.7702 (m) REVERT: A 606 TYR cc_start: 0.7048 (p90) cc_final: 0.6738 (p90) REVERT: B 154 ASN cc_start: 0.8010 (t0) cc_final: 0.7484 (t0) REVERT: B 160 ASP cc_start: 0.7218 (t70) cc_final: 0.6907 (t70) REVERT: B 185 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 369 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.6509 (p0) REVERT: B 420 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8014 (p) REVERT: B 449 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6895 (tm-30) REVERT: B 560 ASP cc_start: 0.8062 (m-30) cc_final: 0.7780 (m-30) REVERT: B 631 TYR cc_start: 0.7721 (m-80) cc_final: 0.7246 (m-80) REVERT: C 41 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 45 ASP cc_start: 0.7063 (m-30) cc_final: 0.6795 (m-30) REVERT: C 65 GLU cc_start: 0.7487 (tt0) cc_final: 0.7280 (tt0) REVERT: C 79 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6933 (mttt) REVERT: C 225 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.6213 (p0) REVERT: C 344 GLU cc_start: 0.7079 (pm20) cc_final: 0.6677 (pm20) REVERT: C 454 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6957 (tm-30) REVERT: C 644 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6493 (mm-30) REVERT: D 41 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6499 (mm-30) REVERT: D 188 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7740 (p-80) REVERT: D 369 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7159 (p0) outliers start: 90 outliers final: 58 residues processed: 565 average time/residue: 1.4013 time to fit residues: 894.8479 Evaluate side-chains 578 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 513 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 567 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 168 optimal weight: 0.0030 chunk 121 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 667 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 385 ASN B 395 GLN B 540 HIS ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS D 639 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21573 Z= 0.211 Angle : 0.583 17.449 29153 Z= 0.302 Chirality : 0.043 0.305 3128 Planarity : 0.004 0.059 3712 Dihedral : 9.984 88.308 3200 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.54 % Favored : 93.42 % Rotamer: Outliers : 3.85 % Allowed : 20.94 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.62 (0.17), residues: 2552 helix: 0.92 (0.16), residues: 1172 sheet: 0.27 (0.35), residues: 256 loop : -2.10 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 425 HIS 0.004 0.001 HIS C 30 PHE 0.037 0.002 PHE B 526 TYR 0.015 0.001 TYR A 666 ARG 0.011 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 517 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 21 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6391 (mpp) REVERT: A 45 ASP cc_start: 0.7283 (m-30) cc_final: 0.6912 (m-30) REVERT: A 60 ILE cc_start: 0.8037 (tp) cc_final: 0.7732 (tt) REVERT: A 301 THR cc_start: 0.7953 (t) cc_final: 0.7715 (m) REVERT: A 606 TYR cc_start: 0.6998 (p90) cc_final: 0.6691 (p90) REVERT: B 160 ASP cc_start: 0.7220 (t70) cc_final: 0.6913 (t70) REVERT: B 185 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 369 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.6454 (p0) REVERT: B 385 ASN cc_start: 0.7468 (m-40) cc_final: 0.7237 (m110) REVERT: B 420 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 446 LEU cc_start: 0.8217 (mt) cc_final: 0.7905 (mt) REVERT: B 449 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 560 ASP cc_start: 0.8073 (m-30) cc_final: 0.7773 (m-30) REVERT: B 631 TYR cc_start: 0.7611 (m-80) cc_final: 0.7181 (m-80) REVERT: C 41 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6599 (mt-10) REVERT: C 45 ASP cc_start: 0.7042 (m-30) cc_final: 0.6771 (m-30) REVERT: C 65 GLU cc_start: 0.7460 (tt0) cc_final: 0.7233 (tt0) REVERT: C 79 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6899 (mttt) REVERT: C 225 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.6185 (p0) REVERT: C 344 GLU cc_start: 0.7102 (pm20) cc_final: 0.6692 (pm20) REVERT: C 454 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6934 (tm-30) REVERT: C 644 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6458 (mm-30) REVERT: D 3 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: D 188 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7696 (p-80) REVERT: D 198 GLU cc_start: 0.6633 (mp0) cc_final: 0.6364 (mp0) REVERT: D 369 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.6976 (p0) REVERT: D 468 ASP cc_start: 0.5563 (OUTLIER) cc_final: 0.5335 (t70) outliers start: 86 outliers final: 57 residues processed: 560 average time/residue: 1.4468 time to fit residues: 915.7319 Evaluate side-chains 577 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 510 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 0.3980 chunk 138 optimal weight: 0.4980 chunk 100 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN A 351 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 667 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 395 GLN B 540 HIS ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21573 Z= 0.216 Angle : 0.591 17.508 29153 Z= 0.305 Chirality : 0.043 0.265 3128 Planarity : 0.004 0.060 3712 Dihedral : 9.898 88.814 3200 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 3.31 % Allowed : 21.52 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % 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: -0.58 (0.17), residues: 2552 helix: 0.94 (0.16), residues: 1174 sheet: 0.31 (0.35), residues: 256 loop : -2.07 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 425 HIS 0.005 0.001 HIS C 30 PHE 0.037 0.002 PHE B 526 TYR 0.016 0.001 TYR D 670 ARG 0.012 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 511 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 21 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6407 (mpp) REVERT: A 45 ASP cc_start: 0.7277 (m-30) cc_final: 0.6909 (m-30) REVERT: A 60 ILE cc_start: 0.8037 (tp) cc_final: 0.7731 (tt) REVERT: A 301 THR cc_start: 0.7957 (t) cc_final: 0.7713 (m) REVERT: A 606 TYR cc_start: 0.7006 (p90) cc_final: 0.6700 (p90) REVERT: B 160 ASP cc_start: 0.7176 (t70) cc_final: 0.6872 (t70) REVERT: B 185 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 215 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6776 (mtm) REVERT: B 368 TYR cc_start: 0.7919 (t80) cc_final: 0.7593 (t80) REVERT: B 369 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.6297 (p0) REVERT: B 420 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7934 (m) REVERT: B 449 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 560 ASP cc_start: 0.8052 (m-30) cc_final: 0.7738 (m-30) REVERT: B 631 TYR cc_start: 0.7610 (m-80) cc_final: 0.7187 (m-80) REVERT: C 41 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6592 (mt-10) REVERT: C 45 ASP cc_start: 0.7068 (m-30) cc_final: 0.6803 (m-30) REVERT: C 65 GLU cc_start: 0.7450 (tt0) cc_final: 0.7216 (tt0) REVERT: C 79 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6897 (mttt) REVERT: C 178 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (m) REVERT: C 225 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.6173 (p0) REVERT: C 344 GLU cc_start: 0.7099 (pm20) cc_final: 0.6695 (pm20) REVERT: C 454 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6923 (tm-30) REVERT: C 644 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6491 (mm-30) REVERT: D 3 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: D 188 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7752 (p-80) REVERT: D 198 GLU cc_start: 0.6655 (mp0) cc_final: 0.6402 (mp0) REVERT: D 369 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7135 (p0) outliers start: 74 outliers final: 55 residues processed: 550 average time/residue: 1.3684 time to fit residues: 851.1760 Evaluate side-chains 569 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 503 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 567 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN A 213 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 16 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 385 ASN B 395 GLN B 540 HIS ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21573 Z= 0.293 Angle : 0.624 17.492 29153 Z= 0.323 Chirality : 0.045 0.263 3128 Planarity : 0.005 0.063 3712 Dihedral : 10.138 87.864 3200 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.56 % Favored : 92.40 % Rotamer: Outliers : 3.27 % Allowed : 21.74 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2552 helix: 0.91 (0.16), residues: 1146 sheet: 0.30 (0.35), residues: 256 loop : -2.14 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 425 HIS 0.007 0.001 HIS C 30 PHE 0.036 0.002 PHE B 526 TYR 0.020 0.002 TYR A 666 ARG 0.012 0.001 ARG A 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 518 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6416 (mpp) REVERT: A 45 ASP cc_start: 0.7263 (m-30) cc_final: 0.6913 (m-30) REVERT: A 60 ILE cc_start: 0.8048 (tp) cc_final: 0.7735 (tt) REVERT: A 301 THR cc_start: 0.7964 (t) cc_final: 0.7734 (m) REVERT: A 606 TYR cc_start: 0.7051 (p90) cc_final: 0.6747 (p90) REVERT: B 160 ASP cc_start: 0.7188 (t70) cc_final: 0.6885 (t70) REVERT: B 185 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 283 LYS cc_start: 0.7305 (mtmm) cc_final: 0.6874 (ptmt) REVERT: B 369 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.6493 (p0) REVERT: B 420 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 449 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6887 (tm-30) REVERT: B 560 ASP cc_start: 0.8056 (m-30) cc_final: 0.7755 (m-30) REVERT: C 17 GLU cc_start: 0.6880 (pp20) cc_final: 0.6665 (pp20) REVERT: C 21 MET cc_start: 0.6942 (mtm) cc_final: 0.6707 (mpp) REVERT: C 41 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6613 (mt-10) REVERT: C 45 ASP cc_start: 0.7142 (m-30) cc_final: 0.6859 (m-30) REVERT: C 79 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6910 (mttt) REVERT: C 178 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8236 (m) REVERT: C 225 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.6244 (p0) REVERT: C 344 GLU cc_start: 0.7067 (pm20) cc_final: 0.6619 (pm20) REVERT: C 454 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6930 (tm-30) REVERT: C 644 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6492 (mm-30) REVERT: D 3 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: D 41 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6511 (mm-30) REVERT: D 188 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7799 (p-80) REVERT: D 198 GLU cc_start: 0.6673 (mp0) cc_final: 0.6356 (mp0) REVERT: D 369 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.7127 (p0) outliers start: 73 outliers final: 53 residues processed: 552 average time/residue: 1.4018 time to fit residues: 874.8769 Evaluate side-chains 572 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 510 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 567 GLU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 178 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 154 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 667 ASN B 16 ASN B 188 HIS B 342 ASN B 385 ASN B 395 GLN B 396 ASN B 540 HIS ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS D 639 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124974 restraints weight = 30726.402| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.88 r_work: 0.3651 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21573 Z= 0.271 Angle : 0.619 17.514 29153 Z= 0.322 Chirality : 0.045 0.252 3128 Planarity : 0.005 0.063 3712 Dihedral : 10.136 87.914 3200 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 3.53 % Allowed : 21.97 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.17), residues: 2552 helix: 0.85 (0.16), residues: 1160 sheet: 0.30 (0.35), residues: 256 loop : -2.19 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 425 HIS 0.007 0.001 HIS C 30 PHE 0.037 0.002 PHE B 526 TYR 0.019 0.002 TYR D 670 ARG 0.011 0.000 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11897.22 seconds wall clock time: 213 minutes 8.35 seconds (12788.35 seconds total)