Starting phenix.real_space_refine on Sat Jan 25 03:20:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.map" model { file = "/net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xj6_38394/01_2025/8xj6_38394.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 S 122 5.16 5 C 14382 2.51 5 N 3858 2.21 5 O 4309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2889 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2865 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2938 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 4752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4752 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 565} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3682 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 438} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 5386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5386 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 647} Chain breaks: 4 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AN2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'AN2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'AN2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13845 SG CYS E 282 71.858 81.459 27.239 1.00151.93 S ATOM 13864 SG CYS E 285 73.663 79.507 24.847 1.00144.96 S ATOM 14094 SG CYS E 314 69.410 77.973 25.486 1.00136.23 S ATOM 19279 SG CYS F 282 80.179 51.549 34.595 1.00154.58 S ATOM 19298 SG CYS F 285 78.301 49.151 33.105 1.00151.86 S ATOM 19510 SG CYS F 314 78.634 53.135 32.549 1.00142.69 S Time building chain proxies: 10.60, per 1000 atoms: 0.47 Number of scatterers: 22688 At special positions: 0 Unit cell: (128.199, 132.508, 156.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 122 16.00 P 15 15.00 O 4309 8.00 N 3858 7.00 C 14382 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: 5.85 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 802 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 285 " pdb="ZN ZN E 802 " - pdb=" ND1 HIS E 290 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 314 " pdb="ZN ZN E 802 " - pdb=" SG CYS E 282 " pdb=" ZN F 802 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 314 " pdb="ZN ZN F 802 " - pdb=" SG CYS F 282 " Number of angles added : 3 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 38 sheets defined 40.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.552A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.780A pdb=" N MET A 547 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.979A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.739A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.561A pdb=" N PHE A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.607A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.574A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 384 removed outlier: 5.142A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.658A pdb=" N LYS B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.890A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 614 through 619 removed outlier: 4.095A pdb=" N MET B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 614 through 619' Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.535A pdb=" N ALA B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.531A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 337 Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.717A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.629A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.602A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU C 460 " --> pdb=" O PRO C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 571 through 579 removed outlier: 3.655A pdb=" N GLU C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.767A pdb=" N LEU C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 693 Processing helix chain 'C' and resid 694 through 698 removed outlier: 3.858A pdb=" N PHE C 698 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 78 through 104 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.906A pdb=" N ASN D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.933A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.021A pdb=" N LEU D 208 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.821A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 571 through 577 Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.649A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.602A pdb=" N PHE D 668 " --> pdb=" O TYR D 664 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 697 removed outlier: 3.576A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 693 " --> pdb=" O PRO D 690 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'E' and resid 242 through 254 Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.578A pdb=" N LEU E 264 " --> pdb=" O PHE E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 457 through 469 Processing helix chain 'E' and resid 476 through 488 removed outlier: 3.612A pdb=" N GLU E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 542 through 546 Processing helix chain 'E' and resid 571 through 579 removed outlier: 3.918A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 641 Processing helix chain 'E' and resid 654 through 661 Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.587A pdb=" N LEU E 669 " --> pdb=" O ARG E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 703 removed outlier: 3.515A pdb=" N ALA E 697 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 27 removed outlier: 3.603A pdb=" N ASN F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 47 Processing helix chain 'F' and resid 78 through 104 Processing helix chain 'F' and resid 108 through 119 removed outlier: 3.703A pdb=" N ASN F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 4.231A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 removed outlier: 3.807A pdb=" N ARG F 167 " --> pdb=" O ASN F 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 168' Processing helix chain 'F' and resid 170 through 174 removed outlier: 3.569A pdb=" N VAL F 173 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.626A pdb=" N LEU F 208 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 310 through 314 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.683A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 431 through 436 removed outlier: 3.970A pdb=" N LYS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR F 436 " --> pdb=" O ASP F 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 431 through 436' Processing helix chain 'F' and resid 455 through 469 removed outlier: 4.279A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 542 through 546 Processing helix chain 'F' and resid 571 through 579 removed outlier: 3.954A pdb=" N GLU F 579 " --> pdb=" O LYS F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 641 removed outlier: 3.505A pdb=" N ALA F 639 " --> pdb=" O GLY F 635 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 661 Processing helix chain 'F' and resid 664 through 680 removed outlier: 3.839A pdb=" N PHE F 668 " --> pdb=" O TYR F 664 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 669 " --> pdb=" O ARG F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 703 Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.607A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 499 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 602 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 501 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 604 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA5, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA6, first strand: chain 'B' and resid 412 through 415 Processing sheet with id=AA7, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.878A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR B 499 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 602 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.365A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.663A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.957A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR C 604 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N PHE C 501 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB4, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.080A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 7 through 8 removed outlier: 3.664A pdb=" N VAL D 212 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 35 removed outlier: 3.868A pdb=" N PHE D 12 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.980A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP D 70 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.532A pdb=" N PHE D 221 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR D 143 " --> pdb=" O PHE D 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AC1, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.635A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 524 through 527 Processing sheet with id=AC4, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AC5, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.295A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 257 through 258 removed outlier: 3.850A pdb=" N SER E 257 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 294 through 299 Processing sheet with id=AC8, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC9, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD1, first strand: chain 'E' and resid 524 through 527 removed outlier: 6.622A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD3, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.108A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 32 through 36 removed outlier: 4.120A pdb=" N PHE F 12 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 73 removed outlier: 10.941A pdb=" N VAL F 65 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASP F 139 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 67 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER F 132 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS F 134 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 124 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 65 through 73 removed outlier: 10.941A pdb=" N VAL F 65 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASP F 139 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE F 67 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR F 219 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 139 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE F 221 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR F 141 " --> pdb=" O PHE F 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 294 through 298 Processing sheet with id=AD8, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AD9, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.698A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.883A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 499 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 628 through 631 789 hydrogen bonds defined for protein. 2262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.62 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6725 1.33 - 1.45: 3325 1.45 - 1.57: 12886 1.57 - 1.69: 27 1.69 - 1.81: 177 Bond restraints: 23140 Sorted by residual: bond pdb=" N3B ANP D 801 " pdb=" PG ANP D 801 " ideal model delta sigma weight residual 1.795 1.594 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.599 0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 1.795 1.600 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" N3B AN2 B 801 " pdb=" PB AN2 B 801 " ideal model delta sigma weight residual 1.701 1.586 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" N3B AN2 E 801 " pdb=" PB AN2 E 801 " ideal model delta sigma weight residual 1.701 1.588 0.113 2.00e-02 2.50e+03 3.18e+01 ... (remaining 23135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 30864 2.58 - 5.17: 394 5.17 - 7.75: 37 7.75 - 10.33: 11 10.33 - 12.92: 9 Bond angle restraints: 31315 Sorted by residual: angle pdb=" C LEU E 321 " pdb=" N ASP E 322 " pdb=" CA ASP E 322 " ideal model delta sigma weight residual 122.94 114.81 8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 139.87 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PA AN2 F 801 " pdb=" O3A AN2 F 801 " pdb=" PB AN2 F 801 " ideal model delta sigma weight residual 123.73 136.64 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PA AN2 B 801 " pdb=" O3A AN2 B 801 " pdb=" PB AN2 B 801 " ideal model delta sigma weight residual 123.73 136.64 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" PB ANP C 801 " pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 126.95 139.83 -12.88 3.00e+00 1.11e-01 1.84e+01 ... (remaining 31310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 13879 32.74 - 65.48: 252 65.48 - 98.22: 68 98.22 - 130.96: 1 130.96 - 163.69: 3 Dihedral angle restraints: 14203 sinusoidal: 5929 harmonic: 8274 Sorted by residual: dihedral pdb=" CA GLU E 579 " pdb=" C GLU E 579 " pdb=" N PRO E 580 " pdb=" CA PRO E 580 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ARG A 570 " pdb=" C ARG A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -128.54 163.69 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 14200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2831 0.054 - 0.109: 610 0.109 - 0.163: 85 0.163 - 0.218: 10 0.218 - 0.272: 4 Chirality restraints: 3540 Sorted by residual: chirality pdb=" C3' ANP D 801 " pdb=" C2' ANP D 801 " pdb=" C4' ANP D 801 " pdb=" O3' ANP D 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP C 801 " pdb=" C2' ANP C 801 " pdb=" C4' ANP C 801 " pdb=" O3' ANP C 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3537 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 558 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO F 559 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 559 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 559 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 455 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO D 456 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 578 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C THR B 578 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 578 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 579 " -0.014 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1810 2.74 - 3.28: 23821 3.28 - 3.82: 37436 3.82 - 4.36: 46564 4.36 - 4.90: 76021 Nonbonded interactions: 185652 Sorted by model distance: nonbonded pdb=" OG1 THR B 507 " pdb=" O2B AN2 B 801 " model vdw 2.196 3.040 nonbonded pdb=" O GLN D 469 " pdb=" NH1 ARG D 479 " model vdw 2.209 3.120 nonbonded pdb=" O GLY F 508 " pdb=" OG1 THR F 511 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG F 514 " pdb=" OE1 GLN F 660 " model vdw 2.222 3.120 nonbonded pdb=" O SER B 455 " pdb=" N MET B 458 " model vdw 2.223 3.120 ... (remaining 185647 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 'A' and (resid 325 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 359 or (resid 360 \ through 361 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 2 through 404 or (resid 405 and (name N or name CA or name C or name O or name C \ B )) or resid 406 through 659 or (resid 660 and (name N or name CA or name C or \ name O or name CB )) or resid 661 through 695)) selection = (chain 'B' and (resid 325 through 342 or (resid 343 through 344 and (name N or n \ ame CA or name C or name O or name CB )) or resid 345 through 404 or (resid 405 \ and (name N or name CA or name C or name O or name CB )) or resid 406 through 53 \ 4 or resid 542 through 561 or resid 566 through 582 or resid 593 through 695)) selection = (chain 'C' and (resid 325 through 343 or (resid 344 and (name N or name CA or na \ me C or name O or name CB )) or resid 345 through 534 or resid 542 through 561 o \ r resid 566 through 582 or resid 593 through 659 or (resid 660 and (name N or na \ me CA or name C or name O or name CB )) or resid 661 through 695)) } ncs_group { reference = (chain 'D' and (resid 5 through 583 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 697 or (resid 69 \ 8 through 700 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 5 through 226 or resid 324 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 534 or \ resid 541 through 700)) } 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: 8.090 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.220 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 23140 Z= 0.341 Angle : 0.748 12.917 31315 Z= 0.400 Chirality : 0.046 0.272 3540 Planarity : 0.005 0.083 3983 Dihedral : 14.554 163.694 8809 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.66 % Favored : 95.84 % Rotamer: Outliers : 0.40 % Allowed : 0.48 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2763 helix: 0.02 (0.17), residues: 971 sheet: 0.16 (0.26), residues: 443 loop : -0.28 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 675 HIS 0.011 0.001 HIS A 548 PHE 0.036 0.002 PHE F 554 TYR 0.018 0.001 TYR B 482 ARG 0.011 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 308 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.8217 (pp20) cc_final: 0.7884 (pp20) REVERT: A 426 MET cc_start: 0.7926 (mmp) cc_final: 0.7616 (mmm) REVERT: A 599 THR cc_start: 0.8316 (m) cc_final: 0.7782 (p) REVERT: B 463 ASN cc_start: 0.8390 (m-40) cc_final: 0.8132 (m-40) REVERT: B 513 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7889 (tptp) REVERT: B 514 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7803 (mtm110) REVERT: B 675 TRP cc_start: 0.8236 (m-10) cc_final: 0.8024 (m-10) REVERT: C 458 MET cc_start: 0.8023 (tmm) cc_final: 0.7695 (tmm) REVERT: C 480 GLU cc_start: 0.7881 (pt0) cc_final: 0.7661 (pp20) REVERT: C 596 ASN cc_start: 0.8155 (t0) cc_final: 0.7560 (m-40) REVERT: D 463 ASN cc_start: 0.9255 (m110) cc_final: 0.9026 (m110) REVERT: D 517 LYS cc_start: 0.8967 (pttp) cc_final: 0.8724 (pttp) REVERT: D 675 TRP cc_start: 0.7937 (m-10) cc_final: 0.7393 (m-10) REVERT: E 399 MET cc_start: 0.8316 (mtm) cc_final: 0.8116 (mtp) REVERT: E 491 CYS cc_start: 0.7060 (p) cc_final: 0.6736 (p) REVERT: E 576 LYS cc_start: 0.8562 (tppt) cc_final: 0.8337 (tppt) REVERT: E 696 PHE cc_start: 0.6220 (m-10) cc_final: 0.5820 (m-80) REVERT: F 89 PHE cc_start: 0.8907 (t80) cc_final: 0.8555 (t80) REVERT: F 99 ARG cc_start: 0.8859 (tpm170) cc_final: 0.8530 (tpm170) REVERT: F 133 PHE cc_start: 0.7167 (m-80) cc_final: 0.6899 (m-80) REVERT: F 197 MET cc_start: 0.4484 (mmm) cc_final: 0.4177 (mmm) REVERT: F 300 ASN cc_start: 0.8356 (p0) cc_final: 0.8017 (t0) REVERT: F 369 LEU cc_start: 0.7938 (mm) cc_final: 0.7650 (mt) REVERT: F 471 LEU cc_start: 0.7738 (mt) cc_final: 0.7451 (tp) outliers start: 10 outliers final: 4 residues processed: 317 average time/residue: 0.3972 time to fit residues: 193.7639 Evaluate side-chains 227 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain F residue 45 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN B 615 ASN C 641 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 352 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.138331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.091287 restraints weight = 54514.960| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.72 r_work: 0.3265 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23140 Z= 0.213 Angle : 0.584 8.818 31315 Z= 0.301 Chirality : 0.044 0.178 3540 Planarity : 0.004 0.055 3983 Dihedral : 10.183 155.644 3224 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.08 % Favored : 96.49 % Rotamer: Outliers : 0.75 % Allowed : 7.45 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2763 helix: 0.39 (0.17), residues: 982 sheet: 0.14 (0.26), residues: 402 loop : -0.32 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 675 HIS 0.004 0.001 HIS F 548 PHE 0.023 0.001 PHE A 357 TYR 0.020 0.001 TYR B 482 ARG 0.007 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8756 (mmp) cc_final: 0.8406 (mmm) REVERT: A 599 THR cc_start: 0.8174 (m) cc_final: 0.7632 (p) REVERT: C 458 MET cc_start: 0.8222 (tmm) cc_final: 0.8005 (tmm) REVERT: C 596 ASN cc_start: 0.8447 (t0) cc_final: 0.7866 (m-40) REVERT: D 152 ARG cc_start: 0.8676 (tpt-90) cc_final: 0.8191 (tpp80) REVERT: D 156 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7899 (mp0) REVERT: D 393 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8782 (tm-30) REVERT: D 463 ASN cc_start: 0.9386 (m110) cc_final: 0.9164 (m110) REVERT: D 554 PHE cc_start: 0.6626 (t80) cc_final: 0.6158 (t80) REVERT: D 675 TRP cc_start: 0.8175 (m-10) cc_final: 0.7487 (m-10) REVERT: D 684 MET cc_start: 0.8069 (tmm) cc_final: 0.7812 (tmm) REVERT: E 299 GLU cc_start: 0.8419 (pp20) cc_final: 0.8187 (pp20) REVERT: E 458 MET cc_start: 0.6310 (tpt) cc_final: 0.5887 (tpt) REVERT: E 462 MET cc_start: 0.8306 (mpp) cc_final: 0.8083 (mpp) REVERT: E 576 LYS cc_start: 0.8632 (tppt) cc_final: 0.8303 (tppt) REVERT: F 89 PHE cc_start: 0.9197 (t80) cc_final: 0.8981 (t80) REVERT: F 99 ARG cc_start: 0.9040 (tpm170) cc_final: 0.8738 (tpm170) REVERT: F 133 PHE cc_start: 0.7456 (m-80) cc_final: 0.6988 (m-80) REVERT: F 300 ASN cc_start: 0.8466 (p0) cc_final: 0.8171 (t0) REVERT: F 369 LEU cc_start: 0.8179 (mm) cc_final: 0.7335 (mt) REVERT: F 471 LEU cc_start: 0.8018 (mt) cc_final: 0.7741 (tp) outliers start: 19 outliers final: 14 residues processed: 266 average time/residue: 0.3680 time to fit residues: 154.7502 Evaluate side-chains 235 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 246 optimal weight: 0.0570 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.137045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089839 restraints weight = 54593.418| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.77 r_work: 0.3235 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23140 Z= 0.235 Angle : 0.568 9.369 31315 Z= 0.292 Chirality : 0.043 0.225 3540 Planarity : 0.004 0.056 3983 Dihedral : 9.233 152.838 3218 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.29 % Favored : 96.31 % Rotamer: Outliers : 1.19 % Allowed : 9.79 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2763 helix: 0.53 (0.17), residues: 982 sheet: 0.04 (0.26), residues: 416 loop : -0.29 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.009 0.001 HIS C 548 PHE 0.022 0.001 PHE A 357 TYR 0.016 0.001 TYR B 482 ARG 0.006 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8745 (mmp) cc_final: 0.8417 (mmm) REVERT: B 426 MET cc_start: 0.7225 (ppp) cc_final: 0.6950 (ppp) REVERT: B 463 ASN cc_start: 0.8535 (m-40) cc_final: 0.8333 (m-40) REVERT: C 480 GLU cc_start: 0.8011 (pt0) cc_final: 0.7519 (pp20) REVERT: C 557 GLU cc_start: 0.8144 (mp0) cc_final: 0.7555 (pt0) REVERT: C 596 ASN cc_start: 0.8699 (t0) cc_final: 0.8341 (m-40) REVERT: C 660 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8564 (mt0) REVERT: D 214 MET cc_start: 0.7860 (mtm) cc_final: 0.7584 (mtp) REVERT: D 384 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9136 (pp) REVERT: D 554 PHE cc_start: 0.6664 (t80) cc_final: 0.6176 (t80) REVERT: D 675 TRP cc_start: 0.8201 (m-10) cc_final: 0.7489 (m-10) REVERT: D 684 MET cc_start: 0.7996 (tmm) cc_final: 0.7743 (tmm) REVERT: E 244 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8845 (pm20) REVERT: E 299 GLU cc_start: 0.8493 (pp20) cc_final: 0.8160 (pp20) REVERT: E 462 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8106 (mpp) REVERT: E 495 LYS cc_start: 0.7849 (mppt) cc_final: 0.7649 (mmtm) REVERT: E 576 LYS cc_start: 0.8626 (tppt) cc_final: 0.8231 (tppt) REVERT: F 133 PHE cc_start: 0.7455 (m-80) cc_final: 0.6854 (m-80) REVERT: F 300 ASN cc_start: 0.8525 (p0) cc_final: 0.8161 (t0) REVERT: F 369 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7464 (mt) REVERT: F 426 MET cc_start: 0.8534 (pmm) cc_final: 0.8321 (pmm) REVERT: F 471 LEU cc_start: 0.8150 (mt) cc_final: 0.7946 (tp) outliers start: 30 outliers final: 16 residues processed: 268 average time/residue: 0.3526 time to fit residues: 149.4014 Evaluate side-chains 241 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 195 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN F 198 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088993 restraints weight = 54749.713| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.80 r_work: 0.3209 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23140 Z= 0.264 Angle : 0.580 8.119 31315 Z= 0.297 Chirality : 0.043 0.198 3540 Planarity : 0.004 0.058 3983 Dihedral : 8.945 152.860 3215 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.51 % Favored : 96.09 % Rotamer: Outliers : 1.35 % Allowed : 12.16 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2763 helix: 0.56 (0.17), residues: 983 sheet: -0.16 (0.25), residues: 431 loop : -0.27 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.004 0.001 HIS F 195 PHE 0.022 0.001 PHE A 357 TYR 0.016 0.001 TYR F 482 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.9041 (mtt) cc_final: 0.8817 (mtt) REVERT: A 426 MET cc_start: 0.8743 (mmp) cc_final: 0.8430 (mmm) REVERT: A 480 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: B 426 MET cc_start: 0.7239 (ppp) cc_final: 0.6655 (ppp) REVERT: B 463 ASN cc_start: 0.8570 (m-40) cc_final: 0.8369 (m-40) REVERT: C 480 GLU cc_start: 0.8042 (pt0) cc_final: 0.7596 (pp20) REVERT: C 660 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8608 (mt0) REVERT: D 214 MET cc_start: 0.7879 (mtm) cc_final: 0.7615 (mtp) REVERT: D 554 PHE cc_start: 0.6759 (t80) cc_final: 0.6196 (t80) REVERT: E 244 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8874 (pm20) REVERT: E 335 ASP cc_start: 0.8355 (t0) cc_final: 0.8116 (t0) REVERT: E 382 GLU cc_start: 0.8522 (mp0) cc_final: 0.8221 (mp0) REVERT: E 431 ASP cc_start: 0.8932 (m-30) cc_final: 0.8467 (t0) REVERT: E 447 ASP cc_start: 0.8241 (t0) cc_final: 0.7933 (m-30) REVERT: E 576 LYS cc_start: 0.8649 (tppt) cc_final: 0.8215 (tppt) REVERT: F 39 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: F 133 PHE cc_start: 0.7406 (m-80) cc_final: 0.6989 (m-80) REVERT: F 369 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7662 (mt) REVERT: F 426 MET cc_start: 0.8517 (pmm) cc_final: 0.8316 (pmm) REVERT: F 579 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7765 (mm-30) outliers start: 34 outliers final: 21 residues processed: 252 average time/residue: 0.3406 time to fit residues: 136.9895 Evaluate side-chains 233 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 274 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 239 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088510 restraints weight = 54753.311| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.73 r_work: 0.3208 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23140 Z= 0.257 Angle : 0.581 10.129 31315 Z= 0.297 Chirality : 0.043 0.149 3540 Planarity : 0.004 0.061 3983 Dihedral : 8.709 153.458 3215 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.26 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 12.72 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2763 helix: 0.55 (0.17), residues: 994 sheet: -0.16 (0.25), residues: 422 loop : -0.34 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.003 0.001 HIS D 109 PHE 0.022 0.001 PHE A 357 TYR 0.021 0.001 TYR F 606 ARG 0.006 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.9057 (mtt) cc_final: 0.8814 (mtt) REVERT: A 426 MET cc_start: 0.8765 (mmp) cc_final: 0.8468 (mmm) REVERT: A 480 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: B 365 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8951 (m) REVERT: B 426 MET cc_start: 0.7268 (ppp) cc_final: 0.6794 (ppp) REVERT: B 463 ASN cc_start: 0.8579 (m-40) cc_final: 0.8375 (m-40) REVERT: B 513 LYS cc_start: 0.7930 (tptp) cc_final: 0.7668 (tptp) REVERT: C 480 GLU cc_start: 0.8084 (pt0) cc_final: 0.7629 (pp20) REVERT: C 557 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7617 (pt0) REVERT: C 660 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8522 (mt0) REVERT: D 1 MET cc_start: 0.5768 (tpp) cc_final: 0.5384 (tpp) REVERT: D 214 MET cc_start: 0.7888 (mtm) cc_final: 0.7595 (mtp) REVERT: D 554 PHE cc_start: 0.6721 (t80) cc_final: 0.6109 (t80) REVERT: D 675 TRP cc_start: 0.8170 (m-10) cc_final: 0.7643 (m-10) REVERT: D 684 MET cc_start: 0.8122 (tmm) cc_final: 0.7788 (tmm) REVERT: E 244 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8786 (pm20) REVERT: E 335 ASP cc_start: 0.8364 (t0) cc_final: 0.8091 (t0) REVERT: E 382 GLU cc_start: 0.8520 (mp0) cc_final: 0.8199 (mp0) REVERT: E 399 MET cc_start: 0.8943 (mtp) cc_final: 0.8580 (mtp) REVERT: E 431 ASP cc_start: 0.8972 (m-30) cc_final: 0.8576 (t0) REVERT: E 462 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8260 (mpp) REVERT: E 576 LYS cc_start: 0.8688 (tppt) cc_final: 0.8237 (tppt) REVERT: F 133 PHE cc_start: 0.7343 (m-80) cc_final: 0.6956 (m-80) REVERT: F 369 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.7620 (mt) REVERT: F 579 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7871 (mm-30) outliers start: 52 outliers final: 28 residues processed: 270 average time/residue: 0.3188 time to fit residues: 139.8431 Evaluate side-chains 244 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 84 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 135 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089982 restraints weight = 54393.276| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.73 r_work: 0.3238 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23140 Z= 0.173 Angle : 0.548 9.327 31315 Z= 0.279 Chirality : 0.042 0.159 3540 Planarity : 0.004 0.072 3983 Dihedral : 8.389 151.603 3215 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.18 % Favored : 96.42 % Rotamer: Outliers : 1.66 % Allowed : 13.59 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2763 helix: 0.68 (0.17), residues: 1005 sheet: -0.03 (0.27), residues: 395 loop : -0.30 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 350 HIS 0.014 0.001 HIS C 548 PHE 0.022 0.001 PHE A 357 TYR 0.012 0.001 TYR B 482 ARG 0.006 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8657 (mmp) cc_final: 0.8368 (mmm) REVERT: A 480 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: B 365 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8924 (m) REVERT: B 426 MET cc_start: 0.7127 (ppp) cc_final: 0.6803 (ppp) REVERT: B 463 ASN cc_start: 0.8551 (m-40) cc_final: 0.8333 (m-40) REVERT: B 513 LYS cc_start: 0.7976 (tptp) cc_final: 0.7696 (tptp) REVERT: C 480 GLU cc_start: 0.8080 (pt0) cc_final: 0.7649 (pp20) REVERT: C 557 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7407 (pt0) REVERT: C 660 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8501 (mt0) REVERT: D 74 ASP cc_start: 0.8374 (t0) cc_final: 0.8144 (t0) REVERT: D 170 ASP cc_start: 0.8723 (t0) cc_final: 0.8408 (t0) REVERT: D 384 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9052 (pp) REVERT: D 554 PHE cc_start: 0.6879 (t80) cc_final: 0.6279 (t80) REVERT: D 675 TRP cc_start: 0.8167 (m-10) cc_final: 0.7437 (m-10) REVERT: D 684 MET cc_start: 0.8076 (tmm) cc_final: 0.7788 (tmm) REVERT: E 244 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8763 (pm20) REVERT: E 245 ASP cc_start: 0.9169 (t70) cc_final: 0.8930 (t70) REVERT: E 335 ASP cc_start: 0.8243 (t0) cc_final: 0.7946 (t0) REVERT: E 382 GLU cc_start: 0.8504 (mp0) cc_final: 0.8171 (mp0) REVERT: E 431 ASP cc_start: 0.8917 (m-30) cc_final: 0.8554 (t0) REVERT: E 462 MET cc_start: 0.8386 (mpp) cc_final: 0.8061 (mpp) REVERT: E 576 LYS cc_start: 0.8660 (tppt) cc_final: 0.8231 (tppt) REVERT: F 133 PHE cc_start: 0.7288 (m-80) cc_final: 0.6947 (m-80) REVERT: F 369 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7457 (tp) REVERT: F 426 MET cc_start: 0.8509 (pmm) cc_final: 0.8256 (pmm) REVERT: F 579 GLU cc_start: 0.8251 (pt0) cc_final: 0.7769 (mm-30) outliers start: 42 outliers final: 28 residues processed: 261 average time/residue: 0.3227 time to fit residues: 137.6339 Evaluate side-chains 247 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 623 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 276 optimal weight: 8.9990 chunk 205 optimal weight: 0.0050 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 264 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 246 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.139109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093010 restraints weight = 54857.680| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.84 r_work: 0.3253 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23140 Z= 0.131 Angle : 0.542 9.816 31315 Z= 0.276 Chirality : 0.042 0.310 3540 Planarity : 0.004 0.070 3983 Dihedral : 7.845 148.398 3215 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.37 % Favored : 96.24 % Rotamer: Outliers : 1.35 % Allowed : 14.18 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2763 helix: 0.86 (0.17), residues: 989 sheet: 0.05 (0.27), residues: 396 loop : -0.17 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 350 HIS 0.003 0.001 HIS D 109 PHE 0.022 0.001 PHE A 357 TYR 0.011 0.001 TYR A 482 ARG 0.005 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8620 (mmp) cc_final: 0.8349 (mmm) REVERT: A 480 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: A 546 ASN cc_start: 0.7773 (m-40) cc_final: 0.6948 (p0) REVERT: B 365 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8853 (m) REVERT: B 463 ASN cc_start: 0.8510 (m-40) cc_final: 0.8302 (m-40) REVERT: B 513 LYS cc_start: 0.7889 (tptp) cc_final: 0.7573 (tptp) REVERT: C 480 GLU cc_start: 0.8059 (pt0) cc_final: 0.7620 (pp20) REVERT: C 557 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7593 (pt0) REVERT: C 660 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8511 (mt0) REVERT: D 1 MET cc_start: 0.5280 (tpp) cc_final: 0.4876 (tpp) REVERT: D 170 ASP cc_start: 0.8656 (t0) cc_final: 0.8290 (t0) REVERT: D 384 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8958 (pp) REVERT: D 554 PHE cc_start: 0.6873 (t80) cc_final: 0.6406 (t80) REVERT: D 675 TRP cc_start: 0.8173 (m-10) cc_final: 0.7481 (m-10) REVERT: D 684 MET cc_start: 0.7991 (tmm) cc_final: 0.7685 (tmm) REVERT: E 244 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8686 (pm20) REVERT: E 245 ASP cc_start: 0.9184 (t70) cc_final: 0.8901 (t70) REVERT: E 365 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8741 (m) REVERT: E 382 GLU cc_start: 0.8484 (mp0) cc_final: 0.8089 (mp0) REVERT: E 431 ASP cc_start: 0.8931 (m-30) cc_final: 0.8556 (t0) REVERT: E 447 ASP cc_start: 0.8098 (t0) cc_final: 0.7615 (t0) REVERT: E 462 MET cc_start: 0.8338 (mpp) cc_final: 0.8069 (mpp) REVERT: E 480 GLU cc_start: 0.8796 (mp0) cc_final: 0.8575 (pm20) REVERT: E 576 LYS cc_start: 0.8681 (tppt) cc_final: 0.8249 (tppt) REVERT: F 133 PHE cc_start: 0.7300 (m-80) cc_final: 0.6998 (m-80) REVERT: F 371 ILE cc_start: 0.9489 (tt) cc_final: 0.9173 (tt) REVERT: F 426 MET cc_start: 0.8541 (pmm) cc_final: 0.8322 (pmm) outliers start: 34 outliers final: 18 residues processed: 288 average time/residue: 0.3205 time to fit residues: 149.6285 Evaluate side-chains 252 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 91 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 227 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.136582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089236 restraints weight = 54801.985| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.76 r_work: 0.3223 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23140 Z= 0.232 Angle : 0.588 12.047 31315 Z= 0.295 Chirality : 0.043 0.280 3540 Planarity : 0.004 0.072 3983 Dihedral : 7.780 149.420 3215 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.33 % Favored : 96.27 % Rotamer: Outliers : 1.62 % Allowed : 14.74 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2763 helix: 0.76 (0.17), residues: 1004 sheet: 0.06 (0.26), residues: 405 loop : -0.32 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 355 HIS 0.004 0.001 HIS B 347 PHE 0.023 0.001 PHE B 668 TYR 0.015 0.001 TYR F 482 ARG 0.005 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8689 (mmp) cc_final: 0.8404 (mmm) REVERT: A 480 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: A 546 ASN cc_start: 0.7791 (m-40) cc_final: 0.6975 (p0) REVERT: B 365 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8964 (m) REVERT: B 513 LYS cc_start: 0.7901 (tptp) cc_final: 0.7627 (tptp) REVERT: C 480 GLU cc_start: 0.8101 (pt0) cc_final: 0.7643 (pp20) REVERT: C 557 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7557 (pt0) REVERT: C 596 ASN cc_start: 0.8663 (t0) cc_final: 0.8447 (m-40) REVERT: C 660 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8486 (mt0) REVERT: D 170 ASP cc_start: 0.8690 (t0) cc_final: 0.8351 (t0) REVERT: D 554 PHE cc_start: 0.6944 (t80) cc_final: 0.6491 (t80) REVERT: D 684 MET cc_start: 0.7914 (tmm) cc_final: 0.7592 (tmm) REVERT: E 244 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8745 (pm20) REVERT: E 365 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8884 (m) REVERT: E 382 GLU cc_start: 0.8561 (mp0) cc_final: 0.8212 (mp0) REVERT: E 431 ASP cc_start: 0.8926 (m-30) cc_final: 0.8598 (t0) REVERT: E 447 ASP cc_start: 0.8209 (t0) cc_final: 0.7824 (m-30) REVERT: E 462 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (mpp) REVERT: E 576 LYS cc_start: 0.8666 (tppt) cc_final: 0.8241 (tptt) REVERT: E 618 MET cc_start: 0.8678 (mmp) cc_final: 0.8113 (tmm) REVERT: F 83 LEU cc_start: 0.7981 (mm) cc_final: 0.7584 (pt) REVERT: F 133 PHE cc_start: 0.7303 (m-80) cc_final: 0.6965 (m-80) REVERT: F 209 PHE cc_start: 0.6729 (p90) cc_final: 0.6467 (p90) REVERT: F 369 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7548 (mt) outliers start: 41 outliers final: 29 residues processed: 253 average time/residue: 0.3440 time to fit residues: 142.8939 Evaluate side-chains 243 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 579 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.091129 restraints weight = 54542.674| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.76 r_work: 0.3255 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23140 Z= 0.159 Angle : 0.577 11.617 31315 Z= 0.287 Chirality : 0.042 0.267 3540 Planarity : 0.004 0.073 3983 Dihedral : 7.654 148.522 3215 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.40 % Favored : 96.24 % Rotamer: Outliers : 1.51 % Allowed : 15.17 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2763 helix: 0.87 (0.17), residues: 988 sheet: -0.03 (0.26), residues: 410 loop : -0.23 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.004 0.000 HIS D 109 PHE 0.022 0.001 PHE B 668 TYR 0.029 0.001 TYR D 664 ARG 0.008 0.000 ARG D 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8625 (mmp) cc_final: 0.8342 (mmm) REVERT: A 480 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: A 546 ASN cc_start: 0.7827 (m-40) cc_final: 0.7030 (p0) REVERT: B 365 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8891 (m) REVERT: C 480 GLU cc_start: 0.8114 (pt0) cc_final: 0.7664 (pp20) REVERT: C 557 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7675 (pt0) REVERT: C 660 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8477 (mt0) REVERT: D 152 ARG cc_start: 0.9016 (tpp80) cc_final: 0.8810 (tpp80) REVERT: D 170 ASP cc_start: 0.8666 (t0) cc_final: 0.8309 (t0) REVERT: D 384 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9010 (pp) REVERT: D 554 PHE cc_start: 0.7058 (t80) cc_final: 0.6678 (t80) REVERT: D 557 GLU cc_start: 0.6771 (pm20) cc_final: 0.6537 (pm20) REVERT: D 684 MET cc_start: 0.7989 (tmm) cc_final: 0.7661 (tmm) REVERT: E 244 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8688 (pm20) REVERT: E 365 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8807 (m) REVERT: E 382 GLU cc_start: 0.8523 (mp0) cc_final: 0.8106 (mp0) REVERT: E 431 ASP cc_start: 0.8931 (m-30) cc_final: 0.8597 (t0) REVERT: E 447 ASP cc_start: 0.8161 (t0) cc_final: 0.7646 (t0) REVERT: E 462 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8160 (mpp) REVERT: E 576 LYS cc_start: 0.8685 (tppt) cc_final: 0.8241 (tppt) REVERT: E 618 MET cc_start: 0.8659 (mmp) cc_final: 0.7955 (tmm) REVERT: E 684 MET cc_start: 0.8127 (tpp) cc_final: 0.7595 (tpp) REVERT: F 133 PHE cc_start: 0.7300 (m-80) cc_final: 0.6952 (m-80) REVERT: F 240 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7191 (p90) outliers start: 38 outliers final: 26 residues processed: 252 average time/residue: 0.3168 time to fit residues: 131.8376 Evaluate side-chains 251 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 113 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 132 optimal weight: 0.0370 chunk 197 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 256 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.136503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089294 restraints weight = 54793.895| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.75 r_work: 0.3226 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23140 Z= 0.212 Angle : 0.594 11.755 31315 Z= 0.295 Chirality : 0.043 0.256 3540 Planarity : 0.004 0.073 3983 Dihedral : 7.689 149.255 3215 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.69 % Favored : 95.95 % Rotamer: Outliers : 1.39 % Allowed : 15.45 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2763 helix: 0.84 (0.17), residues: 993 sheet: 0.02 (0.26), residues: 400 loop : -0.30 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 675 HIS 0.004 0.001 HIS D 109 PHE 0.020 0.001 PHE B 668 TYR 0.014 0.001 TYR F 482 ARG 0.005 0.000 ARG B 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8672 (mmp) cc_final: 0.8393 (mmm) REVERT: A 480 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: A 546 ASN cc_start: 0.7830 (m-40) cc_final: 0.7052 (p0) REVERT: B 365 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8953 (m) REVERT: B 426 MET cc_start: 0.7245 (ppp) cc_final: 0.6729 (ppp) REVERT: C 480 GLU cc_start: 0.8154 (pt0) cc_final: 0.7710 (pp20) REVERT: C 557 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7401 (pt0) REVERT: C 660 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8486 (mt0) REVERT: D 170 ASP cc_start: 0.8672 (t0) cc_final: 0.8330 (t0) REVERT: D 554 PHE cc_start: 0.7046 (t80) cc_final: 0.6651 (t80) REVERT: D 557 GLU cc_start: 0.6852 (pm20) cc_final: 0.6626 (pm20) REVERT: D 684 MET cc_start: 0.7987 (tmm) cc_final: 0.7661 (tmm) REVERT: E 365 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8872 (m) REVERT: E 382 GLU cc_start: 0.8555 (mp0) cc_final: 0.8164 (mp0) REVERT: E 431 ASP cc_start: 0.8955 (m-30) cc_final: 0.8659 (t0) REVERT: E 576 LYS cc_start: 0.8684 (tppt) cc_final: 0.8229 (tptt) REVERT: E 618 MET cc_start: 0.8654 (mmp) cc_final: 0.7938 (tmm) REVERT: E 684 MET cc_start: 0.8283 (tpp) cc_final: 0.7670 (tpp) REVERT: F 133 PHE cc_start: 0.7309 (m-80) cc_final: 0.6938 (m-80) REVERT: F 240 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7221 (p90) outliers start: 35 outliers final: 26 residues processed: 241 average time/residue: 0.3111 time to fit residues: 122.8962 Evaluate side-chains 246 residues out of total 2575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 181 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 246 optimal weight: 0.0020 chunk 234 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 253 optimal weight: 0.0270 overall best weight: 0.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 463 ASN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.138399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092091 restraints weight = 54557.910| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.82 r_work: 0.3266 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23140 Z= 0.146 Angle : 0.579 11.853 31315 Z= 0.289 Chirality : 0.042 0.250 3540 Planarity : 0.004 0.074 3983 Dihedral : 7.527 147.422 3215 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.29 % Favored : 96.34 % Rotamer: Outliers : 1.47 % Allowed : 15.53 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2763 helix: 0.95 (0.17), residues: 982 sheet: 0.01 (0.26), residues: 394 loop : -0.23 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 675 HIS 0.004 0.000 HIS D 109 PHE 0.021 0.001 PHE A 357 TYR 0.013 0.001 TYR D 606 ARG 0.004 0.000 ARG D 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14180.70 seconds wall clock time: 253 minutes 9.66 seconds (15189.66 seconds total)