Starting phenix.real_space_refine on Wed Mar 4 21:43:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.map" model { file = "/net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k36_22650/03_2026/7k36_22650.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 P 6 5.49 5 S 87 5.16 5 C 10561 2.51 5 N 2895 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16613 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 3515 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 681 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'ARG:plan': 17, 'GLU:plan': 28, 'GLN:plan1': 10, 'ASP:plan': 17, 'HIS:plan': 4, 'PHE:plan': 10, 'TRP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 11} Unresolved non-hydrogen planarities: 440 Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2296 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 281} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2360 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 563 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 510 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 457 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 4829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4829 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 576} Chain breaks: 9 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10922 SG CYS H 110 45.332 54.337 99.147 1.00140.34 S ATOM 10989 SG CYS H 119 43.054 56.546 98.471 1.00145.37 S ATOM 10851 SG CYS H 92 32.048 53.692 103.889 1.00171.12 S ATOM 10889 SG CYS H 97 30.821 55.981 106.236 1.00170.80 S Time building chain proxies: 3.79, per 1000 atoms: 0.23 Number of scatterers: 16613 At special positions: 0 Unit cell: (212.48, 98.77, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 87 16.00 P 6 15.00 O 3060 8.00 N 2895 7.00 C 10561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 738.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 127 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 113 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 110 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 119 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 169 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 174 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 97 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 92 " Number of angles added : 4 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 9 sheets defined 66.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 42 removed outlier: 4.077A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.841A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.724A pdb=" N LEU A 89 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.503A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 141 through 155 removed outlier: 4.073A pdb=" N THR A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.749A pdb=" N SER A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 7.246A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 240 through 253 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 258 through 272 removed outlier: 4.061A pdb=" N LYS A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.958A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 4.339A pdb=" N SER A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.572A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 359 through 375 Proline residue: A 367 - end of helix removed outlier: 3.533A pdb=" N ASP A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 395 removed outlier: 3.976A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 434 removed outlier: 3.598A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 441 removed outlier: 4.107A pdb=" N PHE A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.591A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 490 removed outlier: 6.710A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 495 through 513 removed outlier: 4.656A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 5.026A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 569 removed outlier: 4.760A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 116 through 119 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.596A pdb=" N SER C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 135 removed outlier: 3.501A pdb=" N LEU D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 127 removed outlier: 3.624A pdb=" N GLN E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 123 Processing helix chain 'G' and resid 64 through 121 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 37 through 50 removed outlier: 3.990A pdb=" N GLN H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 50 " --> pdb=" O ASN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 66 through 92 removed outlier: 4.182A pdb=" N GLY H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 91 " --> pdb=" O LYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 137 Processing helix chain 'H' and resid 152 through 174 removed outlier: 4.044A pdb=" N LEU H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 185 Processing helix chain 'H' and resid 186 through 199 Processing helix chain 'I' and resid 77 through 84 Processing helix chain 'I' and resid 92 through 109 removed outlier: 4.290A pdb=" N GLU I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 133 Processing helix chain 'I' and resid 137 through 154 Processing helix chain 'I' and resid 161 through 180 Processing helix chain 'I' and resid 180 through 194 removed outlier: 4.061A pdb=" N ALA I 184 " --> pdb=" O GLY I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 213 Processing helix chain 'I' and resid 214 through 233 Processing helix chain 'I' and resid 241 through 253 removed outlier: 3.973A pdb=" N GLY I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 275 removed outlier: 3.584A pdb=" N MET I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 299 Processing helix chain 'I' and resid 300 through 315 Processing helix chain 'I' and resid 323 through 330 Processing helix chain 'I' and resid 429 through 445 Processing helix chain 'I' and resid 460 through 473 removed outlier: 3.739A pdb=" N SER I 466 " --> pdb=" O PRO I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 492 removed outlier: 3.616A pdb=" N VAL I 481 " --> pdb=" O SER I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 514 Processing helix chain 'I' and resid 516 through 532 Processing helix chain 'I' and resid 543 through 548 removed outlier: 3.877A pdb=" N ASP I 547 " --> pdb=" O ILE I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 557 through 593 Processing helix chain 'I' and resid 593 through 607 removed outlier: 3.620A pdb=" N HIS I 603 " --> pdb=" O TYR I 599 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA I 607 " --> pdb=" O HIS I 603 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 617 Processing helix chain 'I' and resid 620 through 627 Processing helix chain 'I' and resid 661 through 679 Processing helix chain 'I' and resid 682 through 692 Processing helix chain 'I' and resid 694 through 702 removed outlier: 3.584A pdb=" N ARG I 700 " --> pdb=" O PRO I 696 " (cutoff:3.500A) Processing helix chain 'I' and resid 706 through 721 removed outlier: 3.588A pdb=" N GLN I 710 " --> pdb=" O GLN I 706 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU I 716 " --> pdb=" O TYR I 712 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL I 719 " --> pdb=" O LYS I 715 " (cutoff:3.500A) Processing helix chain 'I' and resid 724 through 732 removed outlier: 4.186A pdb=" N TRP I 728 " --> pdb=" O LEU I 724 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 743 Processing helix chain 'I' and resid 763 through 784 removed outlier: 3.524A pdb=" N ALA I 773 " --> pdb=" O CYS I 769 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 823 removed outlier: 4.455A pdb=" N TRP I 820 " --> pdb=" O ASN I 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 387 through 392 removed outlier: 6.743A pdb=" N VAL B 711 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 391 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA B 709 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 401 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 454 through 457 removed outlier: 7.108A pdb=" N ASN B 477 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 494 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 505 through 510 Processing sheet with id=AA5, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.708A pdb=" N VAL B 584 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 600 through 605 removed outlier: 4.238A pdb=" N ARG B 602 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 616 " --> pdb=" O HIS B 620 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS B 620 " --> pdb=" O HIS B 616 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS B 633 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 642 through 647 Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.174A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.510A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU C 114 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE C 82 " --> pdb=" O LEU C 114 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3231 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: 2.63 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5497 1.34 - 1.46: 3685 1.46 - 1.58: 7609 1.58 - 1.70: 6 1.70 - 1.82: 135 Bond restraints: 16932 Sorted by residual: bond pdb=" C GLY I 253 " pdb=" N SER I 254 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.07e-02 2.33e+03 6.05e+00 bond pdb=" O12 IHP I 901 " pdb=" P2 IHP I 901 " ideal model delta sigma weight residual 1.675 1.626 0.049 2.00e-02 2.50e+03 5.88e+00 bond pdb=" O15 IHP I 901 " pdb=" P5 IHP I 901 " ideal model delta sigma weight residual 1.675 1.635 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" O32 IHP I 901 " pdb=" P2 IHP I 901 " ideal model delta sigma weight residual 1.537 1.499 0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" O14 IHP I 901 " pdb=" P4 IHP I 901 " ideal model delta sigma weight residual 1.671 1.633 0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 22722 2.56 - 5.11: 235 5.11 - 7.67: 36 7.67 - 10.22: 10 10.22 - 12.78: 1 Bond angle restraints: 23004 Sorted by residual: angle pdb=" N PRO A 354 " pdb=" CA PRO A 354 " pdb=" CB PRO A 354 " ideal model delta sigma weight residual 103.52 110.43 -6.91 9.50e-01 1.11e+00 5.29e+01 angle pdb=" N PRO A 121 " pdb=" CA PRO A 121 " pdb=" CB PRO A 121 " ideal model delta sigma weight residual 103.00 110.45 -7.45 1.10e+00 8.26e-01 4.59e+01 angle pdb=" N PRO A 130 " pdb=" CA PRO A 130 " pdb=" CB PRO A 130 " ideal model delta sigma weight residual 103.39 110.32 -6.93 1.08e+00 8.57e-01 4.12e+01 angle pdb=" N PRO A 328 " pdb=" CA PRO A 328 " pdb=" CB PRO A 328 " ideal model delta sigma weight residual 103.23 110.07 -6.84 1.07e+00 8.73e-01 4.08e+01 angle pdb=" N PRO A 207 " pdb=" CA PRO A 207 " pdb=" CB PRO A 207 " ideal model delta sigma weight residual 103.39 110.14 -6.75 1.08e+00 8.57e-01 3.90e+01 ... (remaining 22999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 9446 24.53 - 49.06: 607 49.06 - 73.59: 77 73.59 - 98.12: 18 98.12 - 122.66: 3 Dihedral angle restraints: 10151 sinusoidal: 3752 harmonic: 6399 Sorted by residual: dihedral pdb=" CA VAL C 87 " pdb=" C VAL C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA THR H 17 " pdb=" C THR H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG C 49 " pdb=" C ARG C 49 " pdb=" N CYS C 50 " pdb=" CA CYS C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 10148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 2646 0.954 - 1.909: 0 1.909 - 2.863: 0 2.863 - 3.817: 0 3.817 - 4.771: 4 Chirality restraints: 2650 Sorted by residual: chirality pdb=" C2 IHP I 901 " pdb=" C1 IHP I 901 " pdb=" C3 IHP I 901 " pdb=" O12 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.52 2.25 -4.77 2.00e-01 2.50e+01 5.69e+02 chirality pdb=" C3 IHP I 901 " pdb=" C2 IHP I 901 " pdb=" C4 IHP I 901 " pdb=" O13 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.34 2.26 -4.60 2.00e-01 2.50e+01 5.28e+02 chirality pdb=" C5 IHP I 901 " pdb=" C4 IHP I 901 " pdb=" C6 IHP I 901 " pdb=" O15 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.42 2.10 -4.52 2.00e-01 2.50e+01 5.10e+02 ... (remaining 2647 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 93 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO H 94 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 94 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 94 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 225 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU I 225 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU I 225 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE I 226 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 606 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 607 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 607 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 607 " 0.025 5.00e-02 4.00e+02 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 2 1.82 - 2.59: 249 2.59 - 3.36: 24101 3.36 - 4.13: 40597 4.13 - 4.90: 74414 Nonbonded interactions: 139363 Sorted by model distance: nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 1.054 2.320 nonbonded pdb=" OD1 ASN C 117 " pdb=" NE2 HIS C 167 " model vdw 1.487 3.120 nonbonded pdb=" CG ASP C 85 " pdb="MN MN C 401 " model vdw 1.860 2.550 nonbonded pdb=" OD1 ASP C 85 " pdb=" ND2 ASN C 117 " model vdw 2.059 3.120 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.076 2.320 ... (remaining 139358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 62 through 125 or (resid 126 through 127 and (name N or na \ me CA or name C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 62 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 102 through 105 and (name N or name CA or \ name C or name O or name CB )) or (resid 106 through 113 and (name N or name CA \ or name C or name O or name CB )) or resid 114 through 115 or (resid 116 through \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throu \ gh 119 or (resid 120 and (name N or name CA or name C or name O or name CB )) or \ resid 121)) selection = chain 'G' } 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: 3.030 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 16940 Z= 0.321 Angle : 0.772 23.850 23008 Z= 0.424 Chirality : 0.184 4.771 2650 Planarity : 0.004 0.050 2938 Dihedral : 16.339 122.656 5975 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 7.26 % Allowed : 17.16 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2121 helix: -0.87 (0.13), residues: 1371 sheet: -1.90 (0.37), residues: 186 loop : -2.84 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 446 TYR 0.017 0.001 TYR I 712 PHE 0.023 0.002 PHE A 538 TRP 0.018 0.002 TRP H 69 HIS 0.007 0.001 HIS I 231 Details of bonding type rmsd covalent geometry : bond 0.00701 (16932) covalent geometry : angle 0.74104 (23004) hydrogen bonds : bond 0.12266 ( 1099) hydrogen bonds : angle 5.82402 ( 3231) metal coordination : bond 0.04376 ( 8) metal coordination : angle 16.39294 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 221 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8215 (ptt-90) cc_final: 0.7980 (ptp90) REVERT: A 427 MET cc_start: 0.8791 (tpt) cc_final: 0.8573 (tmm) REVERT: A 439 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.6816 (p90) REVERT: B 389 LYS cc_start: 0.9085 (tptt) cc_final: 0.8755 (tppt) REVERT: B 418 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8675 (m-70) REVERT: B 440 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7810 (mp0) REVERT: B 463 GLN cc_start: 0.8393 (mp10) cc_final: 0.7987 (mp10) REVERT: B 555 PHE cc_start: 0.7102 (t80) cc_final: 0.6652 (t80) REVERT: B 627 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8599 (mppt) REVERT: B 655 MET cc_start: 0.6598 (mmm) cc_final: 0.6183 (mmm) REVERT: C 188 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: D 81 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8004 (tmm) REVERT: D 82 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8568 (mm-30) REVERT: D 94 GLN cc_start: 0.8907 (tp40) cc_final: 0.8667 (mt0) REVERT: D 105 LYS cc_start: 0.8466 (tptt) cc_final: 0.7544 (tptt) REVERT: E 78 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7795 (ttm-80) REVERT: E 116 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8720 (tpp80) REVERT: F 75 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: F 81 MET cc_start: 0.8170 (ttt) cc_final: 0.7939 (tmm) REVERT: G 75 GLU cc_start: 0.7755 (tt0) cc_final: 0.7197 (tt0) REVERT: H 76 GLN cc_start: 0.8929 (tp40) cc_final: 0.8012 (tp-100) REVERT: H 80 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8626 (mt-10) REVERT: H 148 ILE cc_start: 0.8560 (pt) cc_final: 0.8171 (mm) REVERT: H 193 LYS cc_start: 0.9405 (tttp) cc_final: 0.9095 (mptt) REVERT: I 113 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8152 (mmmm) outliers start: 118 outliers final: 74 residues processed: 329 average time/residue: 0.1665 time to fit residues: 78.1614 Evaluate side-chains 239 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 99 PHE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain I residue 78 TRP Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 258 ASN Chi-restraints excluded: chain I residue 259 ASN Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 HIS Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 481 VAL Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 621 ILE Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 721 THR Chi-restraints excluded: chain I residue 735 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 539 ASN B 477 ASN B 562 HIS B 568 ASN B 599 HIS B 616 HIS ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 70 HIS F 74 HIS G 70 HIS H 82 ASN H 89 GLN H 173 HIS I 570 HIS I 629 ASN I 720 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.080874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055747 restraints weight = 68502.084| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.42 r_work: 0.2951 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16940 Z= 0.153 Angle : 0.617 10.336 23008 Z= 0.310 Chirality : 0.041 0.305 2650 Planarity : 0.004 0.058 2938 Dihedral : 8.439 74.695 2507 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.10 % Allowed : 19.56 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 2121 helix: 0.84 (0.14), residues: 1401 sheet: -1.41 (0.37), residues: 185 loop : -2.12 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 161 TYR 0.017 0.001 TYR H 164 PHE 0.024 0.002 PHE H 77 TRP 0.014 0.001 TRP H 69 HIS 0.011 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00338 (16932) covalent geometry : angle 0.61484 (23004) hydrogen bonds : bond 0.04232 ( 1099) hydrogen bonds : angle 4.44954 ( 3231) metal coordination : bond 0.01277 ( 8) metal coordination : angle 3.64282 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 193 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8378 (ptt-90) cc_final: 0.8119 (ptp90) REVERT: A 427 MET cc_start: 0.9193 (tpt) cc_final: 0.8860 (tmm) REVERT: A 439 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7374 (p90) REVERT: A 521 MET cc_start: 0.9102 (mtt) cc_final: 0.8636 (mtm) REVERT: B 440 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7857 (mp0) REVERT: B 463 GLN cc_start: 0.8564 (mp10) cc_final: 0.8226 (mp10) REVERT: B 490 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9032 (mm-30) REVERT: B 559 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6644 (p0) REVERT: B 563 MET cc_start: 0.6278 (mpp) cc_final: 0.6018 (mpp) REVERT: B 627 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8657 (mppt) REVERT: B 655 MET cc_start: 0.6568 (mmm) cc_final: 0.6139 (mmt) REVERT: B 680 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7103 (m90) REVERT: B 689 TYR cc_start: 0.7321 (m-80) cc_final: 0.6827 (m-80) REVERT: C 132 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: C 188 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8811 (tp30) REVERT: D 81 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8599 (tmm) REVERT: D 82 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8751 (mm-30) REVERT: D 90 ARG cc_start: 0.8995 (ttt180) cc_final: 0.8706 (ttp80) REVERT: D 103 GLU cc_start: 0.9027 (tt0) cc_final: 0.8768 (tt0) REVERT: E 116 ARG cc_start: 0.9065 (tpp80) cc_final: 0.8659 (tpp80) REVERT: F 74 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7552 (m-70) REVERT: F 81 MET cc_start: 0.8196 (ttt) cc_final: 0.7841 (tmm) REVERT: F 120 MET cc_start: 0.6682 (tmm) cc_final: 0.6276 (ppp) REVERT: H 69 TRP cc_start: 0.7394 (OUTLIER) cc_final: 0.6702 (t60) REVERT: H 76 GLN cc_start: 0.8922 (tp40) cc_final: 0.8017 (tp-100) REVERT: H 80 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8714 (mt-10) REVERT: H 148 ILE cc_start: 0.8737 (pt) cc_final: 0.8373 (mp) REVERT: I 96 MET cc_start: 0.8287 (tpt) cc_final: 0.7914 (tpt) REVERT: I 191 MET cc_start: 0.9327 (tmm) cc_final: 0.8706 (tmm) REVERT: I 215 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8105 (p0) REVERT: I 240 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: I 687 MET cc_start: 0.9155 (mmm) cc_final: 0.8937 (mmm) outliers start: 83 outliers final: 46 residues processed: 259 average time/residue: 0.1403 time to fit residues: 54.1193 Evaluate side-chains 224 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 280 HIS Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 481 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 737 SER Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 0.0370 chunk 173 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 162 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 194 optimal weight: 0.0670 chunk 117 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN E 107 GLN H 89 GLN I 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.081237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.053515 restraints weight = 69943.689| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.09 r_work: 0.2991 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16940 Z= 0.153 Angle : 0.579 8.222 23008 Z= 0.294 Chirality : 0.040 0.301 2650 Planarity : 0.004 0.067 2938 Dihedral : 7.653 71.555 2426 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.98 % Allowed : 21.03 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 2121 helix: 1.52 (0.14), residues: 1403 sheet: -1.05 (0.37), residues: 185 loop : -1.95 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 96 TYR 0.017 0.001 TYR H 164 PHE 0.020 0.001 PHE A 538 TRP 0.015 0.001 TRP H 69 HIS 0.010 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00340 (16932) covalent geometry : angle 0.57792 (23004) hydrogen bonds : bond 0.03940 ( 1099) hydrogen bonds : angle 4.23739 ( 3231) metal coordination : bond 0.01275 ( 8) metal coordination : angle 2.43492 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8410 (ptt-90) cc_final: 0.8150 (ptp90) REVERT: A 427 MET cc_start: 0.9204 (tpt) cc_final: 0.8909 (tmm) REVERT: A 439 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7325 (p90) REVERT: A 580 GLN cc_start: 0.9173 (mm110) cc_final: 0.8945 (mm110) REVERT: B 389 LYS cc_start: 0.8958 (tptt) cc_final: 0.8588 (tptp) REVERT: B 440 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 463 GLN cc_start: 0.8681 (mp10) cc_final: 0.8342 (mp10) REVERT: B 478 MET cc_start: 0.8268 (ptp) cc_final: 0.7981 (ptp) REVERT: B 490 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9059 (mm-30) REVERT: B 559 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6476 (p0) REVERT: B 627 LYS cc_start: 0.8827 (mmpt) cc_final: 0.8492 (mmtp) REVERT: B 655 MET cc_start: 0.6356 (mmm) cc_final: 0.5806 (mmt) REVERT: B 680 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.7056 (m90) REVERT: B 689 TYR cc_start: 0.7437 (m-80) cc_final: 0.7013 (m-80) REVERT: C 50 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8179 (m) REVERT: D 69 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8581 (mm) REVERT: D 103 GLU cc_start: 0.8983 (tt0) cc_final: 0.8668 (tt0) REVERT: E 83 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8743 (ttp80) REVERT: E 116 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8638 (tpp80) REVERT: F 81 MET cc_start: 0.8109 (ttt) cc_final: 0.7791 (tmm) REVERT: H 69 TRP cc_start: 0.7510 (OUTLIER) cc_final: 0.6656 (t60) REVERT: H 76 GLN cc_start: 0.8933 (tp40) cc_final: 0.8032 (tp-100) REVERT: H 80 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8702 (mt-10) REVERT: H 118 GLU cc_start: 0.8784 (pm20) cc_final: 0.8424 (tp30) REVERT: H 148 ILE cc_start: 0.8760 (pt) cc_final: 0.8386 (mp) REVERT: H 199 ASN cc_start: 0.8605 (t0) cc_final: 0.7882 (t0) REVERT: I 127 MET cc_start: 0.9416 (mpp) cc_final: 0.8863 (mpp) REVERT: I 168 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.7770 (m-90) REVERT: I 191 MET cc_start: 0.9316 (tmm) cc_final: 0.8612 (tmm) REVERT: I 215 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8039 (p0) REVERT: I 687 MET cc_start: 0.9073 (mmm) cc_final: 0.8853 (mmm) outliers start: 81 outliers final: 48 residues processed: 253 average time/residue: 0.1360 time to fit residues: 51.6228 Evaluate side-chains 223 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 280 HIS Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 481 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 737 SER Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 91 optimal weight: 0.0470 overall best weight: 1.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055545 restraints weight = 69069.940| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.37 r_work: 0.2974 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16940 Z= 0.149 Angle : 0.569 8.083 23008 Z= 0.288 Chirality : 0.040 0.263 2650 Planarity : 0.004 0.062 2938 Dihedral : 7.236 70.351 2414 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.04 % Allowed : 21.59 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2121 helix: 1.81 (0.14), residues: 1401 sheet: -0.93 (0.37), residues: 194 loop : -1.84 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 116 TYR 0.017 0.001 TYR H 164 PHE 0.024 0.001 PHE B 555 TRP 0.017 0.001 TRP H 69 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00334 (16932) covalent geometry : angle 0.56846 (23004) hydrogen bonds : bond 0.03745 ( 1099) hydrogen bonds : angle 4.11519 ( 3231) metal coordination : bond 0.01052 ( 8) metal coordination : angle 1.35386 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 180 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.8177 (ptp90) REVERT: A 427 MET cc_start: 0.9229 (tpt) cc_final: 0.8832 (tmm) REVERT: A 439 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7396 (p90) REVERT: A 528 MET cc_start: 0.9418 (mtp) cc_final: 0.9189 (mtt) REVERT: A 580 GLN cc_start: 0.9233 (mm110) cc_final: 0.8993 (mm110) REVERT: B 389 LYS cc_start: 0.8907 (tptt) cc_final: 0.8534 (tptp) REVERT: B 440 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7922 (mp0) REVERT: B 463 GLN cc_start: 0.8685 (mp10) cc_final: 0.8362 (mp10) REVERT: B 490 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9075 (mm-30) REVERT: B 501 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7146 (p90) REVERT: B 559 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6413 (p0) REVERT: B 627 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8455 (mmtp) REVERT: B 655 MET cc_start: 0.6228 (mmm) cc_final: 0.5919 (mmt) REVERT: B 680 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6968 (m90) REVERT: B 689 TYR cc_start: 0.7438 (m-80) cc_final: 0.7023 (m-80) REVERT: C 245 MET cc_start: 0.8388 (mmt) cc_final: 0.8186 (mmt) REVERT: D 69 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8576 (mm) REVERT: D 103 GLU cc_start: 0.9002 (tt0) cc_final: 0.8722 (tt0) REVERT: E 83 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8775 (ttp80) REVERT: E 111 LYS cc_start: 0.8039 (tttt) cc_final: 0.7832 (tttp) REVERT: E 116 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8581 (tpp80) REVERT: F 81 MET cc_start: 0.8112 (ttt) cc_final: 0.7793 (tmm) REVERT: G 75 GLU cc_start: 0.8117 (tt0) cc_final: 0.7553 (tt0) REVERT: H 69 TRP cc_start: 0.7526 (OUTLIER) cc_final: 0.6743 (t60) REVERT: H 76 GLN cc_start: 0.8964 (tp40) cc_final: 0.8028 (tp-100) REVERT: H 80 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8716 (mt-10) REVERT: H 118 GLU cc_start: 0.8791 (pm20) cc_final: 0.8456 (tp30) REVERT: H 148 ILE cc_start: 0.8795 (pt) cc_final: 0.8426 (mp) REVERT: H 199 ASN cc_start: 0.8616 (t0) cc_final: 0.8071 (t0) REVERT: I 81 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8365 (mm-30) REVERT: I 127 MET cc_start: 0.9442 (mpp) cc_final: 0.8891 (mpp) REVERT: I 168 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.7824 (m-90) REVERT: I 191 MET cc_start: 0.9342 (tmm) cc_final: 0.8627 (tmm) REVERT: I 215 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8024 (p0) REVERT: I 240 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: I 499 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: I 687 MET cc_start: 0.9099 (mmm) cc_final: 0.8860 (mmm) outliers start: 82 outliers final: 47 residues processed: 247 average time/residue: 0.1424 time to fit residues: 52.4663 Evaluate side-chains 221 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 621 ILE Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 737 SER Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 18 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 204 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 516 GLN ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.082316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054936 restraints weight = 68853.265| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.02 r_work: 0.3030 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16940 Z= 0.116 Angle : 0.565 9.844 23008 Z= 0.282 Chirality : 0.040 0.252 2650 Planarity : 0.004 0.059 2938 Dihedral : 6.958 70.829 2408 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.87 % Allowed : 22.69 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2121 helix: 1.98 (0.14), residues: 1406 sheet: -0.70 (0.38), residues: 189 loop : -1.80 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.017 0.001 TYR H 164 PHE 0.038 0.001 PHE H 77 TRP 0.016 0.001 TRP H 69 HIS 0.006 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00256 (16932) covalent geometry : angle 0.56383 (23004) hydrogen bonds : bond 0.03523 ( 1099) hydrogen bonds : angle 3.98888 ( 3231) metal coordination : bond 0.01253 ( 8) metal coordination : angle 2.86271 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8473 (ptt-90) cc_final: 0.8170 (ptp90) REVERT: A 427 MET cc_start: 0.9190 (tpt) cc_final: 0.8884 (tmm) REVERT: A 439 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7337 (p90) REVERT: A 580 GLN cc_start: 0.9253 (mm110) cc_final: 0.8960 (mm110) REVERT: B 440 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7913 (mp0) REVERT: B 463 GLN cc_start: 0.8652 (mp10) cc_final: 0.8219 (mp10) REVERT: B 478 MET cc_start: 0.8083 (ptp) cc_final: 0.7683 (mpp) REVERT: B 490 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9082 (mm-30) REVERT: B 501 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.6907 (p90) REVERT: B 606 HIS cc_start: 0.8646 (t-90) cc_final: 0.8388 (t-90) REVERT: B 627 LYS cc_start: 0.8729 (mmpt) cc_final: 0.8341 (mmtp) REVERT: B 680 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6770 (m90) REVERT: B 689 TYR cc_start: 0.7538 (m-80) cc_final: 0.7087 (m-80) REVERT: D 69 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8560 (mm) REVERT: D 90 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7909 (ttp80) REVERT: D 103 GLU cc_start: 0.8997 (tt0) cc_final: 0.8716 (tt0) REVERT: E 116 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8593 (tpp80) REVERT: F 81 MET cc_start: 0.8089 (ttt) cc_final: 0.7760 (tmm) REVERT: F 83 ARG cc_start: 0.8839 (tmm-80) cc_final: 0.8513 (ttp80) REVERT: G 75 GLU cc_start: 0.8049 (tt0) cc_final: 0.7549 (tt0) REVERT: H 69 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6658 (t60) REVERT: H 73 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: H 76 GLN cc_start: 0.8969 (tp40) cc_final: 0.8551 (mm-40) REVERT: H 77 PHE cc_start: 0.8459 (m-80) cc_final: 0.7742 (m-80) REVERT: H 80 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8935 (mt-10) REVERT: H 118 GLU cc_start: 0.8708 (pm20) cc_final: 0.8494 (tp30) REVERT: H 148 ILE cc_start: 0.8791 (pt) cc_final: 0.8472 (mp) REVERT: H 199 ASN cc_start: 0.8576 (t0) cc_final: 0.8065 (t0) REVERT: I 81 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8287 (mm-30) REVERT: I 127 MET cc_start: 0.9419 (mpp) cc_final: 0.8880 (mpp) REVERT: I 168 TRP cc_start: 0.8343 (OUTLIER) cc_final: 0.7783 (m-90) REVERT: I 191 MET cc_start: 0.9302 (tmm) cc_final: 0.8550 (tmm) REVERT: I 215 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.7881 (p0) REVERT: I 240 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: I 499 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: I 687 MET cc_start: 0.9029 (mmm) cc_final: 0.8800 (mmm) outliers start: 63 outliers final: 41 residues processed: 252 average time/residue: 0.1419 time to fit residues: 53.3618 Evaluate side-chains 225 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 621 ILE Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 181 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.082470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057273 restraints weight = 68500.128| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.43 r_work: 0.3012 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16940 Z= 0.115 Angle : 0.560 9.127 23008 Z= 0.281 Chirality : 0.039 0.194 2650 Planarity : 0.004 0.065 2938 Dihedral : 6.743 70.736 2400 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.18 % Allowed : 22.82 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2121 helix: 2.10 (0.14), residues: 1404 sheet: -0.64 (0.39), residues: 187 loop : -1.76 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 527 TYR 0.017 0.001 TYR H 164 PHE 0.027 0.001 PHE B 555 TRP 0.015 0.001 TRP H 69 HIS 0.010 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00252 (16932) covalent geometry : angle 0.55904 (23004) hydrogen bonds : bond 0.03425 ( 1099) hydrogen bonds : angle 3.94170 ( 3231) metal coordination : bond 0.00942 ( 8) metal coordination : angle 2.05768 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8515 (ptt-90) cc_final: 0.8229 (ptp90) REVERT: A 427 MET cc_start: 0.9229 (tpt) cc_final: 0.8937 (tmm) REVERT: A 439 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7475 (p90) REVERT: A 580 GLN cc_start: 0.9293 (mm110) cc_final: 0.9005 (mm110) REVERT: B 440 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7928 (mp0) REVERT: B 463 GLN cc_start: 0.8689 (mp10) cc_final: 0.8485 (mp10) REVERT: B 490 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9060 (mm-30) REVERT: B 501 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.6807 (p90) REVERT: B 606 HIS cc_start: 0.8632 (t-90) cc_final: 0.8373 (t-90) REVERT: B 627 LYS cc_start: 0.8762 (mmpt) cc_final: 0.8408 (mmtp) REVERT: B 680 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6662 (m90) REVERT: B 689 TYR cc_start: 0.7510 (m-80) cc_final: 0.7057 (m-80) REVERT: C 88 ASP cc_start: 0.7424 (m-30) cc_final: 0.7154 (m-30) REVERT: D 69 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8618 (mm) REVERT: D 90 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7959 (ttp80) REVERT: D 103 GLU cc_start: 0.9018 (tt0) cc_final: 0.8753 (tt0) REVERT: E 83 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8734 (ttp80) REVERT: E 90 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8374 (ttm110) REVERT: E 116 ARG cc_start: 0.9072 (tpp80) cc_final: 0.8639 (tpp80) REVERT: F 81 MET cc_start: 0.8079 (ttt) cc_final: 0.7738 (tmm) REVERT: F 83 ARG cc_start: 0.8823 (tmm-80) cc_final: 0.8577 (ttp80) REVERT: G 75 GLU cc_start: 0.8049 (tt0) cc_final: 0.7529 (tt0) REVERT: H 69 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.6642 (t60) REVERT: H 76 GLN cc_start: 0.8986 (tp40) cc_final: 0.8583 (mm-40) REVERT: H 77 PHE cc_start: 0.8513 (m-80) cc_final: 0.8276 (m-80) REVERT: H 80 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8978 (mt-10) REVERT: H 118 GLU cc_start: 0.8761 (pm20) cc_final: 0.8488 (tp30) REVERT: H 148 ILE cc_start: 0.8813 (pt) cc_final: 0.8476 (mp) REVERT: I 81 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8319 (mm-30) REVERT: I 127 MET cc_start: 0.9475 (mpp) cc_final: 0.9055 (mpp) REVERT: I 168 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7791 (m-90) REVERT: I 191 MET cc_start: 0.9310 (tmm) cc_final: 0.8569 (tmm) REVERT: I 215 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7971 (p0) REVERT: I 240 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: I 499 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: I 687 MET cc_start: 0.9030 (mmm) cc_final: 0.8787 (mmm) REVERT: I 763 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7820 (p0) outliers start: 68 outliers final: 47 residues processed: 237 average time/residue: 0.1402 time to fit residues: 49.3619 Evaluate side-chains 227 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 621 ILE Chi-restraints excluded: chain I residue 737 SER Chi-restraints excluded: chain I residue 763 ASP Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 162 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.081015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055191 restraints weight = 68821.400| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.92 r_work: 0.2994 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16940 Z= 0.209 Angle : 0.613 9.975 23008 Z= 0.309 Chirality : 0.041 0.257 2650 Planarity : 0.004 0.070 2938 Dihedral : 6.779 69.083 2400 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.55 % Allowed : 22.57 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2121 helix: 2.07 (0.14), residues: 1405 sheet: -0.64 (0.39), residues: 195 loop : -1.69 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 96 TYR 0.017 0.001 TYR I 712 PHE 0.028 0.002 PHE B 623 TRP 0.017 0.001 TRP H 69 HIS 0.010 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00476 (16932) covalent geometry : angle 0.61212 (23004) hydrogen bonds : bond 0.03780 ( 1099) hydrogen bonds : angle 4.07049 ( 3231) metal coordination : bond 0.01530 ( 8) metal coordination : angle 2.22176 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8493 (ptt-90) cc_final: 0.8181 (ptp90) REVERT: A 427 MET cc_start: 0.9189 (tpt) cc_final: 0.8935 (tmm) REVERT: A 439 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7409 (p90) REVERT: A 580 GLN cc_start: 0.9282 (mm110) cc_final: 0.9020 (mm110) REVERT: B 389 LYS cc_start: 0.8877 (tptt) cc_final: 0.8480 (tptp) REVERT: B 399 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8375 (m) REVERT: B 440 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7911 (mp0) REVERT: B 462 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9085 (mm-30) REVERT: B 463 GLN cc_start: 0.8733 (mp10) cc_final: 0.8191 (mp10) REVERT: B 478 MET cc_start: 0.8753 (mtt) cc_final: 0.7919 (mpp) REVERT: B 490 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9074 (mm-30) REVERT: B 501 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.6913 (p90) REVERT: B 606 HIS cc_start: 0.8673 (t-90) cc_final: 0.8375 (t-90) REVERT: B 627 LYS cc_start: 0.8779 (mmpt) cc_final: 0.8369 (mmtp) REVERT: B 640 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: B 680 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6737 (m90) REVERT: B 689 TYR cc_start: 0.7431 (m-80) cc_final: 0.6981 (m-80) REVERT: D 69 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (mm) REVERT: D 103 GLU cc_start: 0.9003 (tt0) cc_final: 0.8755 (tt0) REVERT: E 83 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8751 (ttp80) REVERT: E 101 GLN cc_start: 0.8866 (mt0) cc_final: 0.8555 (mp10) REVERT: E 116 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8650 (tpp80) REVERT: F 81 MET cc_start: 0.8118 (ttt) cc_final: 0.7773 (tmm) REVERT: F 100 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6435 (tp) REVERT: H 69 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.6637 (t60) REVERT: H 76 GLN cc_start: 0.8980 (tp40) cc_final: 0.8023 (tp-100) REVERT: H 77 PHE cc_start: 0.8569 (m-80) cc_final: 0.7926 (m-80) REVERT: H 80 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8654 (mt-10) REVERT: H 118 GLU cc_start: 0.8717 (pm20) cc_final: 0.8516 (tp30) REVERT: H 148 ILE cc_start: 0.8814 (pt) cc_final: 0.8401 (mp) REVERT: H 199 ASN cc_start: 0.8679 (t0) cc_final: 0.8061 (t0) REVERT: I 127 MET cc_start: 0.9453 (mpp) cc_final: 0.8974 (mpp) REVERT: I 168 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7832 (m-90) REVERT: I 191 MET cc_start: 0.9318 (tmm) cc_final: 0.8566 (tmm) REVERT: I 215 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7912 (p0) REVERT: I 240 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: I 332 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6118 (ptt-90) REVERT: I 499 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7747 (pm20) outliers start: 74 outliers final: 46 residues processed: 230 average time/residue: 0.1324 time to fit residues: 46.2169 Evaluate side-chains 224 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 735 THR Chi-restraints excluded: chain I residue 737 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 126 optimal weight: 0.0370 chunk 84 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 208 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.082699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057477 restraints weight = 68809.966| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.24 r_work: 0.3029 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16940 Z= 0.113 Angle : 0.589 11.570 23008 Z= 0.293 Chirality : 0.039 0.236 2650 Planarity : 0.004 0.069 2938 Dihedral : 6.508 69.913 2398 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.75 % Allowed : 23.49 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.19), residues: 2121 helix: 2.18 (0.14), residues: 1404 sheet: -0.58 (0.40), residues: 183 loop : -1.61 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.018 0.001 TYR H 164 PHE 0.021 0.001 PHE B 555 TRP 0.015 0.001 TRP H 69 HIS 0.010 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00250 (16932) covalent geometry : angle 0.58762 (23004) hydrogen bonds : bond 0.03409 ( 1099) hydrogen bonds : angle 3.91848 ( 3231) metal coordination : bond 0.00882 ( 8) metal coordination : angle 2.63958 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8538 (ptt-90) cc_final: 0.8261 (ptp90) REVERT: A 427 MET cc_start: 0.9218 (tpt) cc_final: 0.8950 (tmm) REVERT: A 439 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7483 (p90) REVERT: A 580 GLN cc_start: 0.9303 (mm110) cc_final: 0.9026 (mm110) REVERT: B 440 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7951 (mp0) REVERT: B 463 GLN cc_start: 0.8730 (mp10) cc_final: 0.8403 (mp10) REVERT: B 478 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8296 (ptp) REVERT: B 490 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9063 (mm-30) REVERT: B 501 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6802 (p90) REVERT: B 606 HIS cc_start: 0.8671 (t-90) cc_final: 0.8422 (t-90) REVERT: B 627 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8342 (mmtp) REVERT: B 680 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6558 (m90) REVERT: B 689 TYR cc_start: 0.7481 (m-80) cc_final: 0.7029 (m-80) REVERT: C 88 ASP cc_start: 0.7344 (m-30) cc_final: 0.6984 (m-30) REVERT: C 132 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: C 245 MET cc_start: 0.8608 (mmt) cc_final: 0.8343 (mmt) REVERT: D 90 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8072 (ttp80) REVERT: D 103 GLU cc_start: 0.9033 (tt0) cc_final: 0.8758 (tt0) REVERT: E 89 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8769 (mt-10) REVERT: E 90 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8361 (ttm110) REVERT: E 101 GLN cc_start: 0.8887 (mt0) cc_final: 0.8554 (mp10) REVERT: E 116 ARG cc_start: 0.9122 (tpp80) cc_final: 0.8645 (tpp80) REVERT: F 81 MET cc_start: 0.8101 (ttt) cc_final: 0.7746 (tmm) REVERT: F 83 ARG cc_start: 0.8843 (tmm-80) cc_final: 0.8560 (ttp80) REVERT: F 100 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6474 (tp) REVERT: H 69 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6617 (t60) REVERT: H 76 GLN cc_start: 0.8985 (tp40) cc_final: 0.8020 (tp-100) REVERT: H 80 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8679 (mt-10) REVERT: H 118 GLU cc_start: 0.8724 (pm20) cc_final: 0.8442 (tp30) REVERT: H 148 ILE cc_start: 0.8725 (pt) cc_final: 0.8356 (mp) REVERT: I 127 MET cc_start: 0.9463 (mpp) cc_final: 0.9037 (mpp) REVERT: I 168 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.7744 (m-90) REVERT: I 191 MET cc_start: 0.9311 (tmm) cc_final: 0.8532 (tmm) REVERT: I 215 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7956 (p0) REVERT: I 240 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: I 332 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6016 (ptt-90) REVERT: I 763 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7896 (p0) outliers start: 61 outliers final: 36 residues processed: 235 average time/residue: 0.1471 time to fit residues: 51.2123 Evaluate side-chains 216 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 735 THR Chi-restraints excluded: chain I residue 737 SER Chi-restraints excluded: chain I residue 763 ASP Chi-restraints excluded: chain I residue 785 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 150 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 190 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.081538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056459 restraints weight = 69347.206| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.32 r_work: 0.2988 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16940 Z= 0.167 Angle : 0.620 12.712 23008 Z= 0.308 Chirality : 0.041 0.348 2650 Planarity : 0.004 0.069 2938 Dihedral : 6.264 68.605 2392 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.63 % Allowed : 23.99 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2121 helix: 2.19 (0.14), residues: 1405 sheet: -0.76 (0.38), residues: 200 loop : -1.56 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.018 0.001 TYR B 575 PHE 0.018 0.001 PHE B 623 TRP 0.017 0.001 TRP H 69 HIS 0.008 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00385 (16932) covalent geometry : angle 0.61883 (23004) hydrogen bonds : bond 0.03606 ( 1099) hydrogen bonds : angle 3.99900 ( 3231) metal coordination : bond 0.01257 ( 8) metal coordination : angle 2.45873 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8559 (ptt-90) cc_final: 0.8277 (ptp90) REVERT: A 427 MET cc_start: 0.9207 (tpt) cc_final: 0.8963 (tmm) REVERT: A 439 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7484 (p90) REVERT: A 580 GLN cc_start: 0.9314 (mm110) cc_final: 0.9040 (mm110) REVERT: B 440 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7939 (mp0) REVERT: B 463 GLN cc_start: 0.8718 (mp10) cc_final: 0.8388 (mp10) REVERT: B 478 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8255 (ptp) REVERT: B 490 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9069 (mm-30) REVERT: B 501 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.6698 (p90) REVERT: B 606 HIS cc_start: 0.8676 (t-90) cc_final: 0.8386 (t-90) REVERT: B 627 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8409 (mmtp) REVERT: B 680 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6575 (m90) REVERT: B 689 TYR cc_start: 0.7563 (m-80) cc_final: 0.7103 (m-80) REVERT: C 132 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: C 245 MET cc_start: 0.8709 (mmt) cc_final: 0.8097 (mmt) REVERT: D 103 GLU cc_start: 0.9053 (tt0) cc_final: 0.8730 (tt0) REVERT: E 90 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8336 (ttm110) REVERT: E 116 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8638 (tpp80) REVERT: F 81 MET cc_start: 0.8114 (ttt) cc_final: 0.7757 (tmm) REVERT: F 100 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6576 (tp) REVERT: H 69 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.6626 (t60) REVERT: H 76 GLN cc_start: 0.8981 (tp40) cc_final: 0.8026 (tp-100) REVERT: H 77 PHE cc_start: 0.8623 (m-80) cc_final: 0.7985 (m-80) REVERT: H 80 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8647 (mt-10) REVERT: H 118 GLU cc_start: 0.8721 (pm20) cc_final: 0.8425 (tp30) REVERT: H 148 ILE cc_start: 0.8736 (pt) cc_final: 0.8371 (mp) REVERT: I 127 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9041 (mpp) REVERT: I 168 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7814 (m-90) REVERT: I 191 MET cc_start: 0.9330 (tmm) cc_final: 0.8556 (tmm) REVERT: I 215 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7981 (p0) REVERT: I 240 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: I 332 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.5941 (ptt-90) REVERT: I 499 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7662 (pm20) outliers start: 59 outliers final: 43 residues processed: 221 average time/residue: 0.1366 time to fit residues: 45.1554 Evaluate side-chains 222 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 735 THR Chi-restraints excluded: chain I residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 137 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.082384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054955 restraints weight = 69158.873| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.03 r_work: 0.3028 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16940 Z= 0.137 Angle : 0.622 12.180 23008 Z= 0.308 Chirality : 0.040 0.300 2650 Planarity : 0.004 0.068 2938 Dihedral : 6.147 68.582 2391 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.51 % Allowed : 24.11 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 2121 helix: 2.19 (0.14), residues: 1405 sheet: -0.38 (0.41), residues: 177 loop : -1.56 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 116 TYR 0.022 0.001 TYR H 181 PHE 0.018 0.001 PHE B 623 TRP 0.017 0.001 TRP H 69 HIS 0.010 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00316 (16932) covalent geometry : angle 0.62099 (23004) hydrogen bonds : bond 0.03523 ( 1099) hydrogen bonds : angle 3.97622 ( 3231) metal coordination : bond 0.00961 ( 8) metal coordination : angle 2.22449 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8524 (ptt-90) cc_final: 0.8252 (ptp90) REVERT: A 427 MET cc_start: 0.9207 (tpt) cc_final: 0.8960 (tmm) REVERT: A 439 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7490 (p90) REVERT: A 580 GLN cc_start: 0.9309 (mm110) cc_final: 0.9025 (mm110) REVERT: B 440 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 463 GLN cc_start: 0.8729 (mp10) cc_final: 0.8381 (mp10) REVERT: B 478 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8319 (ptp) REVERT: B 490 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9031 (mm-30) REVERT: B 501 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.6720 (p90) REVERT: B 510 TYR cc_start: 0.8486 (t80) cc_final: 0.8258 (t80) REVERT: B 606 HIS cc_start: 0.8738 (t-90) cc_final: 0.8445 (t-90) REVERT: B 627 LYS cc_start: 0.8714 (mmpt) cc_final: 0.8357 (mmtp) REVERT: B 680 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6434 (m90) REVERT: B 689 TYR cc_start: 0.7503 (m-80) cc_final: 0.7093 (m-80) REVERT: C 132 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: C 245 MET cc_start: 0.8657 (mmt) cc_final: 0.8086 (mmt) REVERT: D 103 GLU cc_start: 0.9057 (tt0) cc_final: 0.8766 (tt0) REVERT: E 70 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.8703 (t70) REVERT: E 89 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8752 (mt-10) REVERT: E 90 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8319 (ttm110) REVERT: E 116 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8636 (tpp80) REVERT: F 81 MET cc_start: 0.8117 (ttt) cc_final: 0.7758 (tmm) REVERT: F 83 ARG cc_start: 0.8797 (tmm-80) cc_final: 0.8436 (ttp80) REVERT: F 87 GLU cc_start: 0.9201 (pp20) cc_final: 0.8970 (pp20) REVERT: F 100 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6623 (tp) REVERT: H 69 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6620 (t60) REVERT: H 76 GLN cc_start: 0.8947 (tp40) cc_final: 0.8508 (mm-40) REVERT: H 77 PHE cc_start: 0.8585 (m-80) cc_final: 0.7833 (m-80) REVERT: H 80 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8916 (mt-10) REVERT: H 118 GLU cc_start: 0.8691 (pm20) cc_final: 0.8479 (tp30) REVERT: H 122 ILE cc_start: 0.8985 (mp) cc_final: 0.8556 (tp) REVERT: H 148 ILE cc_start: 0.8786 (pt) cc_final: 0.8246 (mp) REVERT: H 150 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8706 (mm-30) REVERT: I 127 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9024 (mpp) REVERT: I 168 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7798 (m-90) REVERT: I 191 MET cc_start: 0.9295 (tmm) cc_final: 0.8534 (tmm) REVERT: I 215 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7942 (p0) REVERT: I 240 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: I 332 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.5760 (ptt-90) REVERT: I 499 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7694 (pm20) outliers start: 57 outliers final: 42 residues processed: 223 average time/residue: 0.1316 time to fit residues: 44.2519 Evaluate side-chains 230 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 599 HIS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 680 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 73 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 168 TRP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 215 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 310 GLU Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 499 GLU Chi-restraints excluded: chain I residue 544 ILE Chi-restraints excluded: chain I residue 719 VAL Chi-restraints excluded: chain I residue 735 THR Chi-restraints excluded: chain I residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 131 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN H 173 HIS H 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.083244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055955 restraints weight = 69023.955| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.04 r_work: 0.3057 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16940 Z= 0.118 Angle : 0.604 11.036 23008 Z= 0.300 Chirality : 0.040 0.258 2650 Planarity : 0.004 0.069 2938 Dihedral : 6.004 68.491 2391 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.51 % Allowed : 23.99 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2121 helix: 2.25 (0.14), residues: 1401 sheet: -0.22 (0.41), residues: 173 loop : -1.61 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 116 TYR 0.020 0.001 TYR H 164 PHE 0.022 0.001 PHE A 76 TRP 0.017 0.001 TRP H 69 HIS 0.009 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00264 (16932) covalent geometry : angle 0.60352 (23004) hydrogen bonds : bond 0.03339 ( 1099) hydrogen bonds : angle 3.92295 ( 3231) metal coordination : bond 0.00677 ( 8) metal coordination : angle 1.64944 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4818.91 seconds wall clock time: 83 minutes 10.76 seconds (4990.76 seconds total)