Starting phenix.real_space_refine on Fri Mar 6 19:55:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z11_14437/03_2026/7z11_14437.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 143 5.16 5 C 21430 2.51 5 N 5828 2.21 5 O 6645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34079 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5575 Classifications: {'peptide': 727} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 1 Chain: "B" Number of atoms: 5602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5602 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 689} Chain breaks: 1 Chain: "C" Number of atoms: 5611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5611 Classifications: {'peptide': 731} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 690} Chain breaks: 1 Chain: "D" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5630 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 693} Chain breaks: 1 Chain: "E" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5630 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 1 Chain: "F" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5590 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 687} Chain breaks: 1 Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.41, per 1000 atoms: 0.25 Number of scatterers: 34079 At special positions: 0 Unit cell: (140.17, 154.08, 172.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 P 33 15.00 O 6645 8.00 N 5828 7.00 C 21430 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 30 sheets defined 48.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.615A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.780A pdb=" N VAL A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.693A pdb=" N CYS A 142 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 4.070A pdb=" N ILE A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.740A pdb=" N PHE A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.568A pdb=" N ALA A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 360 through 376 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.833A pdb=" N ALA A 380 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 429 through 434 removed outlier: 6.395A pdb=" N SER A 432 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 434 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.511A pdb=" N THR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 487 through 498 removed outlier: 3.659A pdb=" N VAL A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.603A pdb=" N MET A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 538 through 546 Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 592 through 608 removed outlier: 3.573A pdb=" N ILE A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 630 through 649 removed outlier: 3.703A pdb=" N HIS A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 removed outlier: 4.076A pdb=" N ILE A 665 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 685 through 698 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 720 through 739 removed outlier: 3.525A pdb=" N CYS A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.019A pdb=" N ALA A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.719A pdb=" N SER B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.550A pdb=" N CYS B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 143' Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.630A pdb=" N ILE B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.770A pdb=" N ASN B 237 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 removed outlier: 4.572A pdb=" N GLY B 248 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.660A pdb=" N GLU B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Proline residue: B 264 - end of helix removed outlier: 3.575A pdb=" N GLN B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.543A pdb=" N PHE B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 360 through 374 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.760A pdb=" N THR B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.683A pdb=" N LEU B 484 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.653A pdb=" N VAL B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 583 through 587 removed outlier: 4.002A pdb=" N ILE B 586 " --> pdb=" O GLY B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 608 removed outlier: 3.827A pdb=" N ILE B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 removed outlier: 4.331A pdb=" N LEU B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 removed outlier: 3.855A pdb=" N HIS B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.659A pdb=" N ILE B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 701 through 706 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 720 through 739 removed outlier: 3.529A pdb=" N CYS B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 762 through 776 removed outlier: 3.687A pdb=" N ARG B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.666A pdb=" N THR C 48 " --> pdb=" O GLY C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.914A pdb=" N VAL C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 155 removed outlier: 4.181A pdb=" N LYS C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.772A pdb=" N ILE C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 268 through 275 Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 360 through 375 Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 439 through 449 Processing helix chain 'C' and resid 454 through 476 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.802A pdb=" N LEU C 484 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.791A pdb=" N VAL C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 Processing helix chain 'C' and resid 521 through 533 removed outlier: 3.518A pdb=" N MET C 531 " --> pdb=" O LYS C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 538 through 546 Processing helix chain 'C' and resid 562 through 574 Processing helix chain 'C' and resid 582 through 587 removed outlier: 3.854A pdb=" N ILE C 586 " --> pdb=" O GLY C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 608 removed outlier: 3.554A pdb=" N ARG C 596 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 598 " --> pdb=" O SER C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 621 Processing helix chain 'C' and resid 630 through 645 Processing helix chain 'C' and resid 661 through 665 removed outlier: 3.525A pdb=" N ILE C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 671 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 720 through 739 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.578A pdb=" N GLY C 756 " --> pdb=" O LYS C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 774 Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 99 through 107 removed outlier: 3.760A pdb=" N VAL D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 156 removed outlier: 3.708A pdb=" N ILE D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.672A pdb=" N ASN D 237 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 Processing helix chain 'D' and resid 250 through 267 Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.416A pdb=" N PHE D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.511A pdb=" N ILE D 315 " --> pdb=" O GLY D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 Processing helix chain 'D' and resid 346 through 351 removed outlier: 4.228A pdb=" N ILE D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.702A pdb=" N ARG D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 449 Processing helix chain 'D' and resid 454 through 476 Processing helix chain 'D' and resid 480 through 484 Processing helix chain 'D' and resid 487 through 496 Processing helix chain 'D' and resid 500 through 504 removed outlier: 3.891A pdb=" N ARG D 504 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 521 through 533 Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 538 through 546 Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 583 through 587 removed outlier: 4.091A pdb=" N ILE D 586 " --> pdb=" O GLY D 583 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 587 " --> pdb=" O PRO D 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 587' Processing helix chain 'D' and resid 592 through 608 Processing helix chain 'D' and resid 635 through 645 Processing helix chain 'D' and resid 661 through 665 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.658A pdb=" N LEU D 712 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 739 removed outlier: 3.512A pdb=" N GLU D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.567A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 776 removed outlier: 3.721A pdb=" N LEU D 774 " --> pdb=" O GLU D 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 61 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.625A pdb=" N ARG E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 144 through 156 removed outlier: 3.676A pdb=" N ILE E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 247 Processing helix chain 'E' and resid 250 through 266 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 291 through 303 removed outlier: 3.541A pdb=" N SER E 303 " --> pdb=" O VAL E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 337 Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 360 through 375 removed outlier: 3.723A pdb=" N SER E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.313A pdb=" N SER E 394 " --> pdb=" O ARG E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'E' and resid 418 through 427 removed outlier: 3.847A pdb=" N ILE E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 439 through 449 removed outlier: 3.974A pdb=" N LYS E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 480 through 484 Processing helix chain 'E' and resid 487 through 496 Processing helix chain 'E' and resid 521 through 533 Processing helix chain 'E' and resid 533 through 538 Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 564 through 571 Processing helix chain 'E' and resid 596 through 608 Processing helix chain 'E' and resid 617 through 622 Processing helix chain 'E' and resid 635 through 645 Processing helix chain 'E' and resid 661 through 665 Processing helix chain 'E' and resid 666 through 671 removed outlier: 3.768A pdb=" N LEU E 670 " --> pdb=" O ASP E 666 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 671 " --> pdb=" O ALA E 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 666 through 671' Processing helix chain 'E' and resid 685 through 697 removed outlier: 3.617A pdb=" N THR E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 713 Processing helix chain 'E' and resid 723 through 739 removed outlier: 3.598A pdb=" N MET E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 738 " --> pdb=" O ALA E 734 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP E 739 " --> pdb=" O ALA E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 757 removed outlier: 3.608A pdb=" N PHE E 750 " --> pdb=" O GLU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 777 removed outlier: 3.741A pdb=" N LEU E 766 " --> pdb=" O THR E 762 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 775 " --> pdb=" O GLU E 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 48 Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 99 through 107 removed outlier: 3.605A pdb=" N VAL F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 144 through 156 removed outlier: 4.084A pdb=" N ILE F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 250 through 266 Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 268 through 273 removed outlier: 3.708A pdb=" N SER F 272 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 273' Processing helix chain 'F' and resid 291 through 303 Processing helix chain 'F' and resid 321 through 334 removed outlier: 4.245A pdb=" N ALA F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 326 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 334 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 removed outlier: 3.570A pdb=" N ILE F 350 " --> pdb=" O GLU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 374 removed outlier: 4.016A pdb=" N THR F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 Processing helix chain 'F' and resid 396 through 401 removed outlier: 3.637A pdb=" N ARG F 401 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 428 removed outlier: 3.719A pdb=" N PHE F 420 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 Processing helix chain 'F' and resid 454 through 476 removed outlier: 3.931A pdb=" N ASP F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 484 Processing helix chain 'F' and resid 487 through 498 removed outlier: 4.201A pdb=" N VAL F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP F 497 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 521 through 532 Processing helix chain 'F' and resid 532 through 538 Processing helix chain 'F' and resid 538 through 546 Processing helix chain 'F' and resid 562 through 573 Processing helix chain 'F' and resid 582 through 587 removed outlier: 3.687A pdb=" N PHE F 587 " --> pdb=" O GLY F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 606 Processing helix chain 'F' and resid 617 through 621 Processing helix chain 'F' and resid 634 through 647 removed outlier: 4.215A pdb=" N ASP F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY F 646 " --> pdb=" O ASN F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 665 Processing helix chain 'F' and resid 685 through 697 Processing helix chain 'F' and resid 701 through 706 Processing helix chain 'F' and resid 708 through 716 removed outlier: 3.720A pdb=" N LEU F 712 " --> pdb=" O ASP F 708 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP F 714 " --> pdb=" O HIS F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 739 removed outlier: 3.558A pdb=" N CYS F 728 " --> pdb=" O VAL F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 755 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 5.799A pdb=" N ILE A 35 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 98 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 37 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.667A pdb=" N THR A 130 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 183 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 128 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 309 removed outlier: 6.082A pdb=" N HIS A 306 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 343 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 308 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP A 345 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY A 281 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL A 409 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 283 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 7.172A pdb=" N LEU A 579 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP A 616 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 581 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.664A pdb=" N ILE B 35 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 98 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 37 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 178 through 184 removed outlier: 5.276A pdb=" N ILE B 180 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY B 132 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA9, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 306 through 311 removed outlier: 6.120A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 310 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY B 281 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL B 409 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 283 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB3, first strand: chain 'C' and resid 34 through 38 removed outlier: 5.750A pdb=" N ILE C 35 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU C 98 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ARG C 37 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 52 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.328A pdb=" N ILE C 163 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 180 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLN C 165 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 178 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 130 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 183 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS C 128 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.194A pdb=" N HIS C 306 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE C 343 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 308 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP C 345 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 310 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 282 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR C 389 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 284 " --> pdb=" O THR C 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 577 through 581 removed outlier: 6.651A pdb=" N GLY C 552 " --> pdb=" O ARG C 677 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE C 679 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU C 554 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 34 through 38 removed outlier: 6.013A pdb=" N ILE D 35 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU D 98 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG D 37 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 97 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 52 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 72 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.581A pdb=" N ILE D 163 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE D 180 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN D 165 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 178 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR D 130 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA D 183 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS D 128 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.144A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE D 310 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE D 282 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR D 389 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D 284 " --> pdb=" O THR D 389 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU D 283 " --> pdb=" O VAL D 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 577 through 581 removed outlier: 6.329A pdb=" N SER D 611 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 656 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 removed outlier: 5.870A pdb=" N ILE E 35 " --> pdb=" O ILE E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.502A pdb=" N SER E 67 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 163 through 164 removed outlier: 5.148A pdb=" N ILE E 180 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY E 132 " --> pdb=" O ILE E 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AC7, first strand: chain 'E' and resid 306 through 309 removed outlier: 3.916A pdb=" N PHE E 343 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY E 281 " --> pdb=" O GLN E 407 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL E 409 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 283 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 34 through 38 removed outlier: 5.980A pdb=" N ILE F 35 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU F 98 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG F 37 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER F 67 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY F 72 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 163 through 168 removed outlier: 5.192A pdb=" N ILE F 176 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR F 130 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA F 183 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 128 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 133 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AD2, first strand: chain 'F' and resid 306 through 308 removed outlier: 6.648A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 388 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 282 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR F 389 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU F 284 " --> pdb=" O THR F 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 577 through 581 removed outlier: 6.517A pdb=" N ASN F 577 " --> pdb=" O ILE F 612 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE F 614 " --> pdb=" O ASN F 577 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 579 " --> pdb=" O PHE F 614 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER F 611 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL F 656 " --> pdb=" O SER F 611 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) 1424 hydrogen bonds defined for protein. 3921 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: 7.76 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 5877 1.31 - 1.47: 12809 1.47 - 1.63: 15768 1.63 - 1.79: 60 1.79 - 1.95: 173 Bond restraints: 34687 Sorted by residual: bond pdb=" C THR F 323 " pdb=" O THR F 323 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.29e-02 6.01e+03 4.22e+01 bond pdb=" CA LYS D 589 " pdb=" C LYS D 589 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.23e-02 6.61e+03 1.97e+01 bond pdb=" C ILE F 342 " pdb=" O ILE F 342 " ideal model delta sigma weight residual 1.234 1.182 0.052 1.17e-02 7.31e+03 1.95e+01 bond pdb=" N TYR D 590 " pdb=" CA TYR D 590 " ideal model delta sigma weight residual 1.455 1.396 0.059 1.36e-02 5.41e+03 1.85e+01 bond pdb=" N ILE F 342 " pdb=" CA ILE F 342 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.15e-02 7.56e+03 1.73e+01 ... (remaining 34682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 46548 3.26 - 6.53: 461 6.53 - 9.79: 20 9.79 - 13.06: 5 13.06 - 16.32: 2 Bond angle restraints: 47036 Sorted by residual: angle pdb=" CA SER A 611 " pdb=" C SER A 611 " pdb=" O SER A 611 " ideal model delta sigma weight residual 121.36 111.87 9.49 1.06e+00 8.90e-01 8.02e+01 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 114.14 -3.41 4.52e-01 4.89e+00 5.69e+01 angle pdb=" CA ASP D 406 " pdb=" CB ASP D 406 " pdb=" CG ASP D 406 " ideal model delta sigma weight residual 112.60 119.38 -6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " pdb=" N1 AGS F 901 " ideal model delta sigma weight residual 117.53 122.67 -5.14 7.63e-01 1.72e+00 4.53e+01 angle pdb=" CA PRO C 239 " pdb=" N PRO C 239 " pdb=" CD PRO C 239 " ideal model delta sigma weight residual 112.00 102.97 9.03 1.40e+00 5.10e-01 4.16e+01 ... (remaining 47031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 20963 35.65 - 71.31: 338 71.31 - 106.96: 31 106.96 - 142.61: 1 142.61 - 178.27: 2 Dihedral angle restraints: 21335 sinusoidal: 8680 harmonic: 12655 Sorted by residual: dihedral pdb=" CA LEU F 437 " pdb=" C LEU F 437 " pdb=" N ASP F 438 " pdb=" CA ASP F 438 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA ASP F 438 " pdb=" C ASP F 438 " pdb=" N SER F 439 " pdb=" CA SER F 439 " ideal model delta harmonic sigma weight residual 180.00 147.53 32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA GLU B 648 " pdb=" C GLU B 648 " pdb=" N GLU B 649 " pdb=" CA GLU B 649 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 21332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.391: 5454 0.391 - 0.782: 0 0.782 - 1.173: 0 1.173 - 1.563: 0 1.563 - 1.954: 1 Chirality restraints: 5455 Sorted by residual: chirality pdb=" CG LEU E 621 " pdb=" CB LEU E 621 " pdb=" CD1 LEU E 621 " pdb=" CD2 LEU E 621 " both_signs ideal model delta sigma weight residual False -2.59 -0.64 -1.95 2.00e-01 2.50e+01 9.55e+01 chirality pdb=" PA AGS F 901 " pdb=" O2A AGS F 901 " pdb=" O3A AGS F 901 " pdb=" O5' AGS F 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.89 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA LYS D 318 " pdb=" N LYS D 318 " pdb=" C LYS D 318 " pdb=" CB LYS D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 5452 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AGS F 901 " -0.257 2.00e-02 2.50e+03 1.06e-01 3.07e+02 pdb=" C2 AGS F 901 " 0.048 2.00e-02 2.50e+03 pdb=" C4 AGS F 901 " 0.069 2.00e-02 2.50e+03 pdb=" C5 AGS F 901 " 0.031 2.00e-02 2.50e+03 pdb=" C6 AGS F 901 " -0.049 2.00e-02 2.50e+03 pdb=" C8 AGS F 901 " 0.101 2.00e-02 2.50e+03 pdb=" N1 AGS F 901 " -0.044 2.00e-02 2.50e+03 pdb=" N3 AGS F 901 " 0.099 2.00e-02 2.50e+03 pdb=" N6 AGS F 901 " -0.127 2.00e-02 2.50e+03 pdb=" N7 AGS F 901 " 0.061 2.00e-02 2.50e+03 pdb=" N9 AGS F 901 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 263 " -0.099 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO E 264 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO E 264 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO E 264 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 510 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO F 511 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO F 511 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO F 511 " -0.065 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 149 2.47 - 3.08: 25106 3.08 - 3.69: 50448 3.69 - 4.29: 74951 4.29 - 4.90: 124357 Nonbonded interactions: 275011 Sorted by model distance: nonbonded pdb=" OG SER B 720 " pdb=" OE1 GLU B 723 " model vdw 1.867 3.040 nonbonded pdb=" O LEU E 570 " pdb=" OG SER E 574 " model vdw 1.955 3.040 nonbonded pdb=" OD2 ASP E 619 " pdb=" OG1 THR E 659 " model vdw 1.966 3.040 nonbonded pdb=" OG1 THR C 468 " pdb=" OD2 ASP C 490 " model vdw 2.008 3.040 nonbonded pdb=" O ASN B 64 " pdb=" OG SER B 67 " model vdw 2.011 3.040 ... (remaining 275006 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 29 through 774 or resid 902)) selection = (chain 'B' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'C' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'D' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'E' and (resid 29 through 184 or resid 207 through 774 or resid 901)) selection = (chain 'F' and (resid 29 through 184 or resid 207 through 774 or resid 902)) } 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: 1.410 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.150 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.889 34688 Z= 0.539 Angle : 0.800 16.321 47036 Z= 0.481 Chirality : 0.055 1.954 5455 Planarity : 0.007 0.149 6062 Dihedral : 13.990 178.268 13173 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 0.35 % Allowed : 0.46 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4360 helix: -0.28 (0.12), residues: 1679 sheet: -0.84 (0.21), residues: 580 loop : -1.00 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 689 TYR 0.049 0.002 TYR C 319 PHE 0.043 0.002 PHE E 271 TRP 0.012 0.001 TRP E 515 HIS 0.009 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00450 (34687) covalent geometry : angle 0.79966 (47036) hydrogen bonds : bond 0.17448 ( 1424) hydrogen bonds : angle 6.76729 ( 3921) Misc. bond : bond 0.88948 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 802 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7585 (mt) cc_final: 0.7196 (mt) REVERT: A 109 ILE cc_start: 0.8236 (pt) cc_final: 0.7986 (pt) REVERT: A 324 GLU cc_start: 0.6377 (tt0) cc_final: 0.5979 (tt0) REVERT: A 329 ASP cc_start: 0.7655 (t70) cc_final: 0.7288 (t0) REVERT: A 346 GLU cc_start: 0.6686 (mp0) cc_final: 0.6279 (mp0) REVERT: A 371 LEU cc_start: 0.7778 (mt) cc_final: 0.7227 (mt) REVERT: A 389 THR cc_start: 0.7886 (t) cc_final: 0.7685 (t) REVERT: A 448 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7861 (mmpt) REVERT: A 503 MET cc_start: 0.7937 (mmp) cc_final: 0.7676 (mmp) REVERT: A 514 TYR cc_start: 0.8529 (m-80) cc_final: 0.8280 (m-80) REVERT: A 593 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7291 (tp30) REVERT: A 600 GLU cc_start: 0.7233 (tp30) cc_final: 0.6929 (tp30) REVERT: A 601 ILE cc_start: 0.8617 (tt) cc_final: 0.8383 (tt) REVERT: A 695 LYS cc_start: 0.7658 (tmtt) cc_final: 0.7420 (tttt) REVERT: A 715 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: A 717 GLU cc_start: 0.8024 (tp30) cc_final: 0.7529 (tp30) REVERT: B 263 ILE cc_start: 0.8743 (tp) cc_final: 0.8488 (tp) REVERT: B 322 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6588 (mm-30) REVERT: B 377 MET cc_start: -0.0092 (ppp) cc_final: -0.0480 (ppp) REVERT: B 417 ASP cc_start: 0.7481 (m-30) cc_final: 0.7254 (m-30) REVERT: B 484 LEU cc_start: 0.8870 (mt) cc_final: 0.8635 (mp) REVERT: C 95 VAL cc_start: 0.8735 (t) cc_final: 0.8474 (p) REVERT: C 377 MET cc_start: 0.7885 (mtp) cc_final: 0.7535 (mtp) REVERT: C 463 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6817 (mm-30) REVERT: C 754 PHE cc_start: 0.7218 (t80) cc_final: 0.6985 (t80) REVERT: D 128 LYS cc_start: 0.7512 (tttt) cc_final: 0.7271 (tttt) REVERT: D 347 ILE cc_start: 0.8089 (tp) cc_final: 0.7876 (tt) REVERT: D 530 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6762 (mm-30) REVERT: D 548 SER cc_start: 0.8025 (m) cc_final: 0.7682 (p) REVERT: D 589 LYS cc_start: 0.8219 (tttt) cc_final: 0.7996 (tttt) REVERT: D 664 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6314 (mm-30) REVERT: D 699 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8255 (mtpt) REVERT: D 704 GLU cc_start: 0.6423 (mp0) cc_final: 0.6116 (mp0) REVERT: D 769 TYR cc_start: 0.8198 (m-80) cc_final: 0.7852 (m-80) REVERT: E 37 ARG cc_start: 0.6922 (mtp85) cc_final: 0.5455 (tpt90) REVERT: E 103 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.6926 (mtp180) REVERT: E 177 ASP cc_start: 0.5691 (m-30) cc_final: 0.5470 (m-30) REVERT: E 319 TYR cc_start: 0.3521 (OUTLIER) cc_final: 0.3163 (m-80) REVERT: E 320 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5708 (mp) REVERT: E 322 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.5202 (pm20) REVERT: E 399 LEU cc_start: 0.7494 (mt) cc_final: 0.7279 (mt) REVERT: E 453 VAL cc_start: 0.8081 (m) cc_final: 0.7588 (p) REVERT: E 656 VAL cc_start: 0.7704 (m) cc_final: 0.7459 (p) REVERT: E 664 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6413 (mm-30) REVERT: F 244 TYR cc_start: 0.8609 (m-80) cc_final: 0.8350 (m-80) REVERT: F 255 GLU cc_start: 0.5953 (tp30) cc_final: 0.5716 (tp30) REVERT: F 417 ASP cc_start: 0.8033 (t70) cc_final: 0.7144 (t0) REVERT: F 421 ASP cc_start: 0.6926 (m-30) cc_final: 0.6232 (m-30) REVERT: F 430 MET cc_start: 0.5981 (mpp) cc_final: 0.5748 (mtm) REVERT: F 443 LYS cc_start: 0.7744 (mppt) cc_final: 0.7441 (mptt) REVERT: F 456 ASP cc_start: 0.7540 (m-30) cc_final: 0.7291 (m-30) REVERT: F 468 THR cc_start: 0.7543 (m) cc_final: 0.7336 (m) REVERT: F 643 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6422 (mm-30) REVERT: F 770 GLU cc_start: 0.6258 (tp30) cc_final: 0.6006 (tp30) outliers start: 13 outliers final: 1 residues processed: 813 average time/residue: 0.2670 time to fit residues: 328.3039 Evaluate side-chains 729 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 725 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 319 TYR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 319 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN B 426 GLN C 311 ASN C 338 GLN C 353 ASN C 407 GLN D 634 ASN E 56 ASN E 107 ASN E 301 ASN E 332 ASN F 301 ASN F 304 ASN F 642 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.172194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136281 restraints weight = 48859.731| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.22 r_work: 0.3477 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 34688 Z= 0.143 Angle : 0.648 8.647 47036 Z= 0.336 Chirality : 0.046 0.195 5455 Planarity : 0.005 0.083 6062 Dihedral : 9.730 171.119 4951 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 1.30 % Allowed : 7.12 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4360 helix: 0.34 (0.12), residues: 1735 sheet: -0.59 (0.21), residues: 588 loop : -0.71 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 603 TYR 0.019 0.001 TYR D 768 PHE 0.019 0.001 PHE F 578 TRP 0.009 0.001 TRP E 515 HIS 0.012 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00330 (34687) covalent geometry : angle 0.64829 (47036) hydrogen bonds : bond 0.04518 ( 1424) hydrogen bonds : angle 5.10182 ( 3921) Misc. bond : bond 0.00523 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 746 time to evaluate : 1.272 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 98 LEU cc_start: 0.7729 (mt) cc_final: 0.7416 (mt) REVERT: A 159 MET cc_start: 0.6731 (ptp) cc_final: 0.6440 (ptp) REVERT: A 265 LEU cc_start: 0.8399 (mt) cc_final: 0.8179 (mt) REVERT: A 294 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8034 (ttt) REVERT: A 329 ASP cc_start: 0.8250 (t70) cc_final: 0.7854 (t0) REVERT: A 345 ASP cc_start: 0.7586 (t70) cc_final: 0.7102 (t0) REVERT: A 346 GLU cc_start: 0.7334 (mp0) cc_final: 0.7089 (mp0) REVERT: A 371 LEU cc_start: 0.7877 (mt) cc_final: 0.7646 (mt) REVERT: A 408 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 593 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7566 (tp30) REVERT: A 595 GLU cc_start: 0.8236 (mp0) cc_final: 0.7934 (mp0) REVERT: A 600 GLU cc_start: 0.8168 (tp30) cc_final: 0.7921 (tp30) REVERT: A 695 LYS cc_start: 0.7990 (tmtt) cc_final: 0.7695 (tttt) REVERT: A 711 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 263 ILE cc_start: 0.8948 (tp) cc_final: 0.8695 (tp) REVERT: B 322 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7278 (mm-30) REVERT: B 751 GLU cc_start: 0.8073 (tp30) cc_final: 0.7764 (mm-30) REVERT: C 453 VAL cc_start: 0.8577 (p) cc_final: 0.8327 (t) REVERT: C 463 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 128 LYS cc_start: 0.7763 (tttt) cc_final: 0.7512 (tttt) REVERT: D 319 TYR cc_start: 0.8268 (m-80) cc_final: 0.8025 (m-80) REVERT: D 347 ILE cc_start: 0.8514 (tp) cc_final: 0.8299 (tt) REVERT: D 363 GLU cc_start: 0.6869 (mp0) cc_final: 0.6567 (mp0) REVERT: D 527 LYS cc_start: 0.8673 (mttm) cc_final: 0.8389 (mttm) REVERT: D 589 LYS cc_start: 0.8494 (tttt) cc_final: 0.8231 (tttt) REVERT: D 664 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7827 (mm-30) REVERT: D 699 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8350 (mtpt) REVERT: D 704 GLU cc_start: 0.7014 (mp0) cc_final: 0.6546 (mp0) REVERT: D 768 TYR cc_start: 0.7895 (t80) cc_final: 0.7458 (t80) REVERT: E 37 ARG cc_start: 0.7019 (mtp85) cc_final: 0.5753 (tpt90) REVERT: E 107 ASN cc_start: 0.7632 (t0) cc_final: 0.6693 (t0) REVERT: E 269 THR cc_start: 0.7702 (p) cc_final: 0.6690 (m) REVERT: E 419 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7189 (mtt90) REVERT: E 448 LYS cc_start: 0.8036 (pptt) cc_final: 0.7835 (pptt) REVERT: E 463 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6573 (mm-30) REVERT: E 492 GLU cc_start: 0.6583 (mt-10) cc_final: 0.5724 (mt-10) REVERT: E 554 LEU cc_start: 0.6731 (tp) cc_final: 0.6520 (tp) REVERT: E 656 VAL cc_start: 0.7871 (m) cc_final: 0.7577 (p) REVERT: E 664 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6404 (mm-30) REVERT: E 679 ILE cc_start: 0.7361 (pt) cc_final: 0.7136 (pt) REVERT: F 162 MET cc_start: 0.6641 (mmm) cc_final: 0.6229 (mmm) REVERT: F 274 PHE cc_start: 0.6703 (m-10) cc_final: 0.6470 (m-10) REVERT: F 280 ARG cc_start: 0.6992 (mtp-110) cc_final: 0.6709 (ttm170) REVERT: F 292 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7722 (mtmm) REVERT: F 417 ASP cc_start: 0.8329 (t70) cc_final: 0.7856 (t0) REVERT: F 419 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7526 (mtm180) REVERT: F 427 PHE cc_start: 0.7609 (m-80) cc_final: 0.7263 (m-80) REVERT: F 430 MET cc_start: 0.6296 (mpp) cc_final: 0.4938 (ptp) REVERT: F 503 MET cc_start: 0.8129 (mmm) cc_final: 0.7842 (mmm) REVERT: F 585 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5609 (pt0) REVERT: F 596 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7015 (mtp85) REVERT: F 643 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6883 (mm-30) REVERT: F 730 GLU cc_start: 0.7932 (tp30) cc_final: 0.7460 (tp30) REVERT: F 738 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7217 (tm-30) outliers start: 48 outliers final: 26 residues processed: 767 average time/residue: 0.2646 time to fit residues: 309.7620 Evaluate side-chains 717 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 689 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 461 CYS Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 466 MET Chi-restraints excluded: chain F residue 585 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 259 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 267 GLN B 338 GLN B 353 ASN B 356 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 338 GLN C 353 ASN D 301 ASN D 353 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 304 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133060 restraints weight = 49307.053| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.22 r_work: 0.3426 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 34688 Z= 0.280 Angle : 0.690 8.458 47036 Z= 0.356 Chirality : 0.050 0.237 5455 Planarity : 0.005 0.068 6062 Dihedral : 9.796 168.554 4944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 2.00 % Allowed : 10.42 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4360 helix: 0.32 (0.12), residues: 1731 sheet: -0.67 (0.21), residues: 604 loop : -0.82 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 671 TYR 0.023 0.002 TYR A 337 PHE 0.022 0.002 PHE D 578 TRP 0.007 0.002 TRP E 515 HIS 0.011 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00674 (34687) covalent geometry : angle 0.68996 (47036) hydrogen bonds : bond 0.04931 ( 1424) hydrogen bonds : angle 5.02245 ( 3921) Misc. bond : bond 0.00419 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 723 time to evaluate : 1.255 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 47 GLU cc_start: 0.7532 (pm20) cc_final: 0.7264 (pm20) REVERT: A 261 ILE cc_start: 0.8683 (mm) cc_final: 0.8335 (mt) REVERT: A 329 ASP cc_start: 0.8385 (t70) cc_final: 0.7999 (t0) REVERT: A 345 ASP cc_start: 0.7648 (t70) cc_final: 0.6821 (t0) REVERT: A 346 GLU cc_start: 0.7353 (mp0) cc_final: 0.7021 (mp0) REVERT: A 452 TYR cc_start: 0.8851 (m-80) cc_final: 0.8646 (m-10) REVERT: A 695 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7773 (tttt) REVERT: A 711 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7336 (tp30) REVERT: A 715 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8214 (mtm-85) REVERT: A 751 GLU cc_start: 0.8247 (tp30) cc_final: 0.7832 (tp30) REVERT: B 263 ILE cc_start: 0.8960 (tp) cc_final: 0.8708 (tp) REVERT: B 322 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 406 ASP cc_start: 0.7920 (m-30) cc_final: 0.7659 (m-30) REVERT: B 510 MET cc_start: 0.8226 (mtp) cc_final: 0.7940 (mtp) REVERT: B 562 SER cc_start: 0.8265 (p) cc_final: 0.7925 (p) REVERT: B 723 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 377 MET cc_start: 0.8152 (mtp) cc_final: 0.7760 (mtp) REVERT: D 33 GLU cc_start: 0.7275 (pt0) cc_final: 0.7057 (pt0) REVERT: D 109 ILE cc_start: 0.8018 (mt) cc_final: 0.7690 (mt) REVERT: D 128 LYS cc_start: 0.7794 (tttt) cc_final: 0.7421 (tttt) REVERT: D 231 GLN cc_start: 0.8150 (mp-120) cc_final: 0.7731 (mm-40) REVERT: D 319 TYR cc_start: 0.8310 (m-80) cc_final: 0.8100 (m-80) REVERT: D 363 GLU cc_start: 0.7113 (mp0) cc_final: 0.6735 (mp0) REVERT: D 490 ASP cc_start: 0.7318 (m-30) cc_final: 0.7085 (m-30) REVERT: D 503 MET cc_start: 0.7632 (mmt) cc_final: 0.7190 (tpp) REVERT: D 589 LYS cc_start: 0.8618 (tttt) cc_final: 0.8391 (tttt) REVERT: D 664 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 704 GLU cc_start: 0.7124 (mp0) cc_final: 0.6676 (mp0) REVERT: D 739 ASP cc_start: 0.6190 (t0) cc_final: 0.5889 (t70) REVERT: E 37 ARG cc_start: 0.7158 (mtp85) cc_final: 0.5603 (tpt90) REVERT: E 262 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 269 THR cc_start: 0.7792 (p) cc_final: 0.6767 (m) REVERT: E 407 GLN cc_start: 0.7459 (mp10) cc_final: 0.6660 (mp10) REVERT: E 419 ARG cc_start: 0.7478 (mtm180) cc_final: 0.7115 (mtt180) REVERT: E 448 LYS cc_start: 0.8111 (pptt) cc_final: 0.7815 (pptt) REVERT: E 495 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6019 (pmm) REVERT: E 530 GLU cc_start: 0.7501 (tp30) cc_final: 0.7046 (tp30) REVERT: E 656 VAL cc_start: 0.7818 (m) cc_final: 0.7529 (p) REVERT: E 723 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: E 730 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6678 (tm-30) REVERT: F 162 MET cc_start: 0.6852 (mmm) cc_final: 0.6068 (mmm) REVERT: F 244 TYR cc_start: 0.8633 (m-80) cc_final: 0.8378 (m-80) REVERT: F 252 LYS cc_start: 0.8512 (mppt) cc_final: 0.7950 (mtmm) REVERT: F 258 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7827 (mmmm) REVERT: F 417 ASP cc_start: 0.8354 (t70) cc_final: 0.7893 (t0) REVERT: F 465 VAL cc_start: 0.8736 (t) cc_final: 0.8438 (t) REVERT: F 510 MET cc_start: 0.5735 (mpp) cc_final: 0.5485 (mpp) REVERT: F 564 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7803 (t) REVERT: F 585 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5775 (pt0) REVERT: F 596 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7020 (mtp85) REVERT: F 612 ILE cc_start: 0.7575 (mt) cc_final: 0.7365 (mt) REVERT: F 661 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: F 730 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: F 738 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7370 (tm-30) REVERT: F 770 GLU cc_start: 0.7248 (tp30) cc_final: 0.6800 (tp30) outliers start: 74 outliers final: 45 residues processed: 750 average time/residue: 0.2520 time to fit residues: 288.2448 Evaluate side-chains 757 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 706 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 461 CYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 723 GLU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 730 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 332 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 435 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 377 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 281 optimal weight: 0.3980 chunk 299 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 ASN B 390 ASN C 39 HIS C 311 ASN C 338 GLN C 353 ASN D 634 ASN E 107 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN F 301 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135748 restraints weight = 48824.657| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.24 r_work: 0.3469 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34688 Z= 0.125 Angle : 0.582 8.542 47036 Z= 0.300 Chirality : 0.044 0.188 5455 Planarity : 0.005 0.069 6062 Dihedral : 9.436 168.556 4944 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 2.19 % Allowed : 12.31 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4360 helix: 0.71 (0.13), residues: 1737 sheet: -0.61 (0.21), residues: 603 loop : -0.63 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 603 TYR 0.018 0.001 TYR F 337 PHE 0.021 0.001 PHE E 217 TRP 0.006 0.001 TRP E 515 HIS 0.010 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00287 (34687) covalent geometry : angle 0.58221 (47036) hydrogen bonds : bond 0.03755 ( 1424) hydrogen bonds : angle 4.69771 ( 3921) Misc. bond : bond 0.00190 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 728 time to evaluate : 1.267 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: A 47 GLU cc_start: 0.7568 (pm20) cc_final: 0.7292 (pm20) REVERT: A 329 ASP cc_start: 0.8309 (t70) cc_final: 0.7950 (t0) REVERT: A 335 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7910 (tpp80) REVERT: A 345 ASP cc_start: 0.7565 (t70) cc_final: 0.6748 (t0) REVERT: A 346 GLU cc_start: 0.7360 (mp0) cc_final: 0.7050 (mp0) REVERT: A 695 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7673 (tttt) REVERT: A 711 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7275 (tp30) REVERT: A 715 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: A 751 GLU cc_start: 0.8200 (tp30) cc_final: 0.7827 (mm-30) REVERT: B 263 ILE cc_start: 0.8918 (tp) cc_final: 0.8659 (tp) REVERT: B 322 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 406 ASP cc_start: 0.7759 (m-30) cc_final: 0.7522 (m-30) REVERT: B 562 SER cc_start: 0.8139 (p) cc_final: 0.7782 (p) REVERT: B 751 GLU cc_start: 0.8176 (tp30) cc_final: 0.7894 (mm-30) REVERT: B 770 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 210 TYR cc_start: 0.5623 (m-80) cc_final: 0.5339 (m-10) REVERT: C 377 MET cc_start: 0.8091 (mtp) cc_final: 0.7703 (mtp) REVERT: C 453 VAL cc_start: 0.8501 (p) cc_final: 0.8197 (m) REVERT: C 600 GLU cc_start: 0.8271 (tp30) cc_final: 0.8044 (tp30) REVERT: C 742 VAL cc_start: 0.6505 (OUTLIER) cc_final: 0.6241 (t) REVERT: C 755 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8048 (ttmm) REVERT: D 109 ILE cc_start: 0.7970 (mt) cc_final: 0.7661 (mt) REVERT: D 128 LYS cc_start: 0.7771 (tttt) cc_final: 0.7521 (tttt) REVERT: D 231 GLN cc_start: 0.8153 (mp-120) cc_final: 0.7926 (mp-120) REVERT: D 485 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7670 (mmtp) REVERT: D 490 ASP cc_start: 0.7151 (m-30) cc_final: 0.6934 (m-30) REVERT: D 503 MET cc_start: 0.7390 (mmt) cc_final: 0.6890 (tpp) REVERT: D 527 LYS cc_start: 0.8711 (mttm) cc_final: 0.8427 (mttm) REVERT: D 534 LEU cc_start: 0.8408 (tp) cc_final: 0.8024 (tp) REVERT: D 589 LYS cc_start: 0.8570 (tttt) cc_final: 0.8350 (tttt) REVERT: D 664 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7794 (mm-30) REVERT: D 694 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8477 (mtpt) REVERT: D 699 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8586 (mtpt) REVERT: D 704 GLU cc_start: 0.7143 (mp0) cc_final: 0.6702 (mp0) REVERT: D 739 ASP cc_start: 0.6171 (t0) cc_final: 0.5936 (t70) REVERT: D 746 GLU cc_start: 0.6920 (tp30) cc_final: 0.6570 (tp30) REVERT: E 37 ARG cc_start: 0.6987 (mtp85) cc_final: 0.5459 (tpt90) REVERT: E 107 ASN cc_start: 0.7613 (t0) cc_final: 0.6966 (t0) REVERT: E 262 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7152 (mm-30) REVERT: E 269 THR cc_start: 0.7778 (p) cc_final: 0.6658 (m) REVERT: E 396 ASP cc_start: 0.8153 (t0) cc_final: 0.7874 (t0) REVERT: E 410 GLU cc_start: 0.7201 (tp30) cc_final: 0.6839 (tp30) REVERT: E 448 LYS cc_start: 0.8115 (pptt) cc_final: 0.7831 (pptt) REVERT: E 495 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.5935 (pmm) REVERT: E 530 GLU cc_start: 0.7453 (tp30) cc_final: 0.6936 (tp30) REVERT: E 656 VAL cc_start: 0.7732 (m) cc_final: 0.7448 (p) REVERT: E 730 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6623 (tm-30) REVERT: F 162 MET cc_start: 0.6887 (mmm) cc_final: 0.6619 (mmm) REVERT: F 244 TYR cc_start: 0.8616 (m-80) cc_final: 0.8388 (m-80) REVERT: F 252 LYS cc_start: 0.8395 (mppt) cc_final: 0.7818 (mtmm) REVERT: F 258 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7752 (mmmm) REVERT: F 280 ARG cc_start: 0.6993 (mtp-110) cc_final: 0.6733 (ttm170) REVERT: F 399 LEU cc_start: 0.8375 (mp) cc_final: 0.8164 (mm) REVERT: F 417 ASP cc_start: 0.8315 (t70) cc_final: 0.7805 (t0) REVERT: F 419 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7438 (mtm180) REVERT: F 430 MET cc_start: 0.6402 (mpp) cc_final: 0.6112 (ptp) REVERT: F 463 GLU cc_start: 0.7807 (tp30) cc_final: 0.7540 (tp30) REVERT: F 564 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7708 (t) REVERT: F 573 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 585 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5835 (pt0) REVERT: F 596 ARG cc_start: 0.7459 (mtp85) cc_final: 0.6942 (mtp85) REVERT: F 738 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7354 (tm-30) outliers start: 81 outliers final: 39 residues processed: 770 average time/residue: 0.2567 time to fit residues: 303.1576 Evaluate side-chains 732 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 689 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 762 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 260 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 389 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 431 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 338 GLN B 353 ASN B 356 ASN C 311 ASN C 338 GLN D 353 ASN D 634 ASN E 233 ASN ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.171648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135615 restraints weight = 48833.428| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.23 r_work: 0.3464 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34688 Z= 0.136 Angle : 0.583 9.794 47036 Z= 0.298 Chirality : 0.045 0.395 5455 Planarity : 0.005 0.059 6062 Dihedral : 9.361 166.830 4942 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.27 % Allowed : 13.13 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4360 helix: 0.84 (0.13), residues: 1750 sheet: -0.49 (0.21), residues: 594 loop : -0.59 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 603 TYR 0.016 0.001 TYR D 768 PHE 0.033 0.001 PHE E 578 TRP 0.006 0.001 TRP E 515 HIS 0.009 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00321 (34687) covalent geometry : angle 0.58259 (47036) hydrogen bonds : bond 0.03706 ( 1424) hydrogen bonds : angle 4.59794 ( 3921) Misc. bond : bond 0.00194 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 712 time to evaluate : 1.328 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 47 GLU cc_start: 0.7616 (pm20) cc_final: 0.7182 (pm20) REVERT: A 294 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8012 (ttt) REVERT: A 329 ASP cc_start: 0.8303 (t70) cc_final: 0.7951 (t0) REVERT: A 335 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7904 (tpp80) REVERT: A 345 ASP cc_start: 0.7533 (t70) cc_final: 0.6682 (t0) REVERT: A 346 GLU cc_start: 0.7395 (mp0) cc_final: 0.7143 (mp0) REVERT: A 695 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7655 (tttt) REVERT: A 744 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8440 (ptmt) REVERT: A 751 GLU cc_start: 0.8165 (tp30) cc_final: 0.7612 (tp30) REVERT: B 71 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7320 (m) REVERT: B 263 ILE cc_start: 0.8927 (tp) cc_final: 0.8661 (tp) REVERT: B 322 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7363 (mm-30) REVERT: B 406 ASP cc_start: 0.7735 (m-30) cc_final: 0.7466 (m-30) REVERT: B 562 SER cc_start: 0.8161 (p) cc_final: 0.7829 (p) REVERT: B 751 GLU cc_start: 0.8136 (tp30) cc_final: 0.7857 (mm-30) REVERT: C 162 MET cc_start: 0.6850 (mtt) cc_final: 0.6519 (mtt) REVERT: C 210 TYR cc_start: 0.5793 (m-80) cc_final: 0.5482 (m-10) REVERT: C 377 MET cc_start: 0.8117 (mtp) cc_final: 0.7727 (mtp) REVERT: C 600 GLU cc_start: 0.8212 (tp30) cc_final: 0.8009 (tp30) REVERT: C 671 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8162 (ptm-80) REVERT: C 742 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6308 (t) REVERT: C 755 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8057 (ttmm) REVERT: D 109 ILE cc_start: 0.7965 (mt) cc_final: 0.7688 (mt) REVERT: D 128 LYS cc_start: 0.7769 (tttt) cc_final: 0.7530 (tttt) REVERT: D 231 GLN cc_start: 0.8158 (mp-120) cc_final: 0.7904 (mp-120) REVERT: D 363 GLU cc_start: 0.7094 (mp0) cc_final: 0.6619 (mp0) REVERT: D 503 MET cc_start: 0.7328 (mmt) cc_final: 0.6770 (tpp) REVERT: D 534 LEU cc_start: 0.8395 (tp) cc_final: 0.8088 (tp) REVERT: D 548 SER cc_start: 0.8173 (m) cc_final: 0.7839 (p) REVERT: D 589 LYS cc_start: 0.8593 (tttt) cc_final: 0.8388 (tttt) REVERT: D 664 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7775 (mm-30) REVERT: D 694 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8499 (mtpt) REVERT: D 704 GLU cc_start: 0.7092 (mp0) cc_final: 0.6669 (mp0) REVERT: D 739 ASP cc_start: 0.6211 (t0) cc_final: 0.5954 (t0) REVERT: D 746 GLU cc_start: 0.6808 (tp30) cc_final: 0.6441 (tp30) REVERT: E 37 ARG cc_start: 0.6965 (mtp85) cc_final: 0.5437 (tpt90) REVERT: E 103 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.6567 (mtp180) REVERT: E 107 ASN cc_start: 0.7669 (t0) cc_final: 0.7140 (t0) REVERT: E 177 ASP cc_start: 0.6060 (m-30) cc_final: 0.5816 (m-30) REVERT: E 269 THR cc_start: 0.7804 (p) cc_final: 0.6685 (m) REVERT: E 396 ASP cc_start: 0.8207 (t0) cc_final: 0.7919 (t0) REVERT: E 448 LYS cc_start: 0.8132 (pptt) cc_final: 0.7844 (pptt) REVERT: E 463 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6532 (mm-30) REVERT: E 495 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.5865 (pmm) REVERT: E 656 VAL cc_start: 0.7758 (m) cc_final: 0.7442 (p) REVERT: E 664 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6180 (mm-30) REVERT: E 746 GLU cc_start: 0.6344 (tt0) cc_final: 0.5670 (mm-30) REVERT: F 162 MET cc_start: 0.6792 (mmm) cc_final: 0.6101 (mmm) REVERT: F 262 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6926 (mt-10) REVERT: F 365 ARG cc_start: 0.5077 (ttm110) cc_final: 0.4846 (ttm110) REVERT: F 399 LEU cc_start: 0.8355 (mp) cc_final: 0.8146 (mm) REVERT: F 417 ASP cc_start: 0.8294 (t70) cc_final: 0.8043 (t0) REVERT: F 419 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: F 430 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5994 (ptp) REVERT: F 463 GLU cc_start: 0.7855 (tp30) cc_final: 0.7567 (tp30) REVERT: F 564 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7662 (t) REVERT: F 573 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7586 (tm-30) REVERT: F 585 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5776 (pt0) REVERT: F 596 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6973 (mtp85) REVERT: F 717 GLU cc_start: 0.8512 (tp30) cc_final: 0.7524 (tp30) REVERT: F 738 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7338 (tm-30) outliers start: 84 outliers final: 51 residues processed: 753 average time/residue: 0.2626 time to fit residues: 303.1374 Evaluate side-chains 751 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 692 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 430 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 255 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 418 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 186 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 338 GLN B 356 ASN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 338 GLN C 353 ASN D 301 ASN D 353 ASN D 634 ASN E 233 ASN E 660 ASN F 301 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.170316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134236 restraints weight = 48670.435| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.23 r_work: 0.3450 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34688 Z= 0.191 Angle : 0.612 10.399 47036 Z= 0.312 Chirality : 0.046 0.443 5455 Planarity : 0.005 0.058 6062 Dihedral : 9.383 168.419 4942 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.76 % Favored : 94.22 % Rotamer: Outliers : 2.65 % Allowed : 13.45 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4360 helix: 0.79 (0.13), residues: 1752 sheet: -0.50 (0.21), residues: 589 loop : -0.64 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 603 TYR 0.016 0.001 TYR D 768 PHE 0.019 0.001 PHE F 578 TRP 0.006 0.001 TRP E 515 HIS 0.010 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00460 (34687) covalent geometry : angle 0.61163 (47036) hydrogen bonds : bond 0.03992 ( 1424) hydrogen bonds : angle 4.62939 ( 3921) Misc. bond : bond 0.00277 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 713 time to evaluate : 1.303 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 47 GLU cc_start: 0.7631 (pm20) cc_final: 0.7211 (pm20) REVERT: A 329 ASP cc_start: 0.8330 (t70) cc_final: 0.7966 (t0) REVERT: A 452 TYR cc_start: 0.8861 (m-80) cc_final: 0.8651 (m-10) REVERT: A 695 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7718 (tttt) REVERT: A 711 GLU cc_start: 0.7769 (tp30) cc_final: 0.7391 (tp30) REVERT: A 715 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: A 744 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8452 (ptmt) REVERT: B 71 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7339 (m) REVERT: B 252 LYS cc_start: 0.8563 (tptp) cc_final: 0.8295 (tptt) REVERT: B 263 ILE cc_start: 0.8903 (tp) cc_final: 0.8646 (tp) REVERT: B 322 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 406 ASP cc_start: 0.7794 (m-30) cc_final: 0.7534 (m-30) REVERT: B 562 SER cc_start: 0.8228 (p) cc_final: 0.7922 (p) REVERT: C 162 MET cc_start: 0.6927 (mtt) cc_final: 0.6649 (mtt) REVERT: C 210 TYR cc_start: 0.6037 (m-80) cc_final: 0.5794 (m-80) REVERT: C 377 MET cc_start: 0.8149 (mtp) cc_final: 0.7685 (mtp) REVERT: C 600 GLU cc_start: 0.8188 (tp30) cc_final: 0.7984 (tp30) REVERT: C 671 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8272 (ptm-80) REVERT: C 742 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.6305 (t) REVERT: C 755 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8101 (ttmm) REVERT: D 109 ILE cc_start: 0.8031 (mt) cc_final: 0.7763 (mt) REVERT: D 128 LYS cc_start: 0.7781 (tttt) cc_final: 0.7541 (tttt) REVERT: D 170 LYS cc_start: 0.6554 (mmtt) cc_final: 0.6289 (mmtp) REVERT: D 231 GLN cc_start: 0.8213 (mp-120) cc_final: 0.7554 (mp-120) REVERT: D 363 GLU cc_start: 0.7212 (mp0) cc_final: 0.6733 (mp0) REVERT: D 534 LEU cc_start: 0.8437 (tp) cc_final: 0.8129 (tp) REVERT: D 589 LYS cc_start: 0.8644 (tttt) cc_final: 0.8442 (tttt) REVERT: D 664 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7849 (mm-30) REVERT: D 694 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8579 (mtpt) REVERT: D 704 GLU cc_start: 0.7133 (mp0) cc_final: 0.6691 (mp0) REVERT: D 746 GLU cc_start: 0.6824 (tp30) cc_final: 0.6497 (tp30) REVERT: E 37 ARG cc_start: 0.6997 (mtp85) cc_final: 0.5553 (tpt90) REVERT: E 107 ASN cc_start: 0.7722 (t0) cc_final: 0.7370 (t0) REVERT: E 177 ASP cc_start: 0.5973 (m-30) cc_final: 0.5705 (m-30) REVERT: E 269 THR cc_start: 0.7899 (p) cc_final: 0.6772 (m) REVERT: E 389 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7272 (m) REVERT: E 396 ASP cc_start: 0.8181 (t0) cc_final: 0.7853 (t0) REVERT: E 407 GLN cc_start: 0.7808 (mt0) cc_final: 0.7236 (mp10) REVERT: E 419 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7011 (mtm-85) REVERT: E 448 LYS cc_start: 0.8068 (pptt) cc_final: 0.7790 (pptt) REVERT: E 495 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5760 (pmm) REVERT: E 530 GLU cc_start: 0.7523 (tp30) cc_final: 0.7037 (tp30) REVERT: E 656 VAL cc_start: 0.7802 (m) cc_final: 0.7499 (p) REVERT: E 664 GLU cc_start: 0.6729 (mm-30) cc_final: 0.5463 (tp30) REVERT: E 730 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6671 (tm-30) REVERT: F 262 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7011 (mt-10) REVERT: F 280 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6974 (ttm170) REVERT: F 399 LEU cc_start: 0.8359 (mp) cc_final: 0.8081 (mm) REVERT: F 417 ASP cc_start: 0.8419 (t70) cc_final: 0.8103 (t0) REVERT: F 419 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: F 430 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6013 (ptp) REVERT: F 463 GLU cc_start: 0.7870 (tp30) cc_final: 0.7593 (tp30) REVERT: F 497 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7576 (t0) REVERT: F 503 MET cc_start: 0.8374 (mmm) cc_final: 0.8168 (mmm) REVERT: F 523 GLU cc_start: 0.7720 (mp0) cc_final: 0.7405 (mp0) REVERT: F 564 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7754 (t) REVERT: F 573 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 585 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5759 (pt0) REVERT: F 596 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6997 (mtp85) REVERT: F 641 LEU cc_start: 0.6303 (mm) cc_final: 0.5782 (mm) REVERT: F 717 GLU cc_start: 0.8513 (tp30) cc_final: 0.7493 (tp30) REVERT: F 738 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7395 (tm-30) REVERT: F 770 GLU cc_start: 0.7238 (tp30) cc_final: 0.6784 (tp30) outliers start: 98 outliers final: 67 residues processed: 757 average time/residue: 0.2629 time to fit residues: 303.9132 Evaluate side-chains 774 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 698 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 430 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 762 THR Chi-restraints excluded: chain F residue 765 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 152 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 374 optimal weight: 30.0000 chunk 367 optimal weight: 10.0000 chunk 416 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 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 135 GLN A 138 ASN B 356 ASN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 338 GLN D 301 ASN D 450 HIS E 233 ASN E 301 ASN F 301 ASN F 304 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.171264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135102 restraints weight = 48941.587| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.25 r_work: 0.3457 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34688 Z= 0.146 Angle : 0.585 9.362 47036 Z= 0.298 Chirality : 0.045 0.383 5455 Planarity : 0.005 0.061 6062 Dihedral : 9.219 168.037 4942 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.52 % Allowed : 14.18 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.13), residues: 4360 helix: 0.90 (0.13), residues: 1750 sheet: -0.50 (0.21), residues: 600 loop : -0.56 (0.15), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 596 TYR 0.016 0.001 TYR D 768 PHE 0.029 0.001 PHE E 217 TRP 0.006 0.001 TRP E 515 HIS 0.012 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00348 (34687) covalent geometry : angle 0.58466 (47036) hydrogen bonds : bond 0.03671 ( 1424) hydrogen bonds : angle 4.54202 ( 3921) Misc. bond : bond 0.00222 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 718 time to evaluate : 1.544 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 47 GLU cc_start: 0.7639 (pm20) cc_final: 0.7220 (pm20) REVERT: A 304 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7192 (m110) REVERT: A 329 ASP cc_start: 0.8299 (t70) cc_final: 0.7944 (t0) REVERT: A 695 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7684 (tttt) REVERT: A 711 GLU cc_start: 0.7782 (tp30) cc_final: 0.7412 (tp30) REVERT: A 715 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7971 (mtp85) REVERT: A 744 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8407 (ptmt) REVERT: A 751 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 71 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7353 (m) REVERT: B 252 LYS cc_start: 0.8591 (tptp) cc_final: 0.8315 (tptt) REVERT: B 263 ILE cc_start: 0.8894 (tp) cc_final: 0.8638 (tp) REVERT: B 322 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 406 ASP cc_start: 0.7801 (m-30) cc_final: 0.7555 (m-30) REVERT: B 562 SER cc_start: 0.8178 (p) cc_final: 0.7860 (p) REVERT: C 162 MET cc_start: 0.7019 (mtt) cc_final: 0.6743 (mtt) REVERT: C 210 TYR cc_start: 0.6062 (m-80) cc_final: 0.5782 (m-80) REVERT: C 377 MET cc_start: 0.8167 (mtp) cc_final: 0.7718 (mtp) REVERT: C 671 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8250 (ptm-80) REVERT: C 742 VAL cc_start: 0.6535 (OUTLIER) cc_final: 0.6286 (t) REVERT: C 755 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8059 (ttmm) REVERT: D 109 ILE cc_start: 0.8004 (mt) cc_final: 0.7748 (mt) REVERT: D 128 LYS cc_start: 0.7789 (tttt) cc_final: 0.7557 (tttt) REVERT: D 231 GLN cc_start: 0.8218 (mp-120) cc_final: 0.7560 (mp-120) REVERT: D 363 GLU cc_start: 0.7150 (mp0) cc_final: 0.6685 (mp0) REVERT: D 527 LYS cc_start: 0.8695 (mttm) cc_final: 0.8428 (mttm) REVERT: D 534 LEU cc_start: 0.8375 (tp) cc_final: 0.7998 (tp) REVERT: D 589 LYS cc_start: 0.8633 (tttt) cc_final: 0.8407 (tttt) REVERT: D 664 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7795 (mm-30) REVERT: D 694 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8524 (mtpt) REVERT: D 699 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8567 (mtpt) REVERT: D 704 GLU cc_start: 0.7145 (mp0) cc_final: 0.6670 (mp0) REVERT: E 37 ARG cc_start: 0.6931 (mtp85) cc_final: 0.5406 (tpt90) REVERT: E 107 ASN cc_start: 0.7658 (t0) cc_final: 0.7305 (t0) REVERT: E 177 ASP cc_start: 0.5962 (m-30) cc_final: 0.5695 (m-30) REVERT: E 269 THR cc_start: 0.7909 (p) cc_final: 0.6775 (m) REVERT: E 297 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7917 (mmm160) REVERT: E 389 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7313 (m) REVERT: E 407 GLN cc_start: 0.7747 (mt0) cc_final: 0.7113 (mp10) REVERT: E 419 ARG cc_start: 0.7543 (mtm180) cc_final: 0.6878 (mtm-85) REVERT: E 436 VAL cc_start: 0.6145 (OUTLIER) cc_final: 0.5217 (t) REVERT: E 448 LYS cc_start: 0.8077 (pptt) cc_final: 0.7783 (pptt) REVERT: E 463 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6505 (mm-30) REVERT: E 495 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5633 (pmm) REVERT: E 530 GLU cc_start: 0.7484 (tp30) cc_final: 0.7112 (tp30) REVERT: E 656 VAL cc_start: 0.7762 (m) cc_final: 0.7427 (p) REVERT: E 664 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6192 (mm-30) REVERT: E 746 GLU cc_start: 0.6400 (tt0) cc_final: 0.5717 (mm-30) REVERT: F 162 MET cc_start: 0.6760 (mmm) cc_final: 0.6278 (mmm) REVERT: F 258 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7743 (mmmm) REVERT: F 262 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6903 (mt-10) REVERT: F 280 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6844 (ttm170) REVERT: F 292 LYS cc_start: 0.8522 (mtmm) cc_final: 0.7982 (mtmm) REVERT: F 399 LEU cc_start: 0.8305 (mp) cc_final: 0.8063 (mm) REVERT: F 417 ASP cc_start: 0.8414 (t70) cc_final: 0.8085 (t0) REVERT: F 419 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7417 (mtm180) REVERT: F 430 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6060 (ptp) REVERT: F 463 GLU cc_start: 0.7850 (tp30) cc_final: 0.7554 (tp30) REVERT: F 497 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7551 (t0) REVERT: F 523 GLU cc_start: 0.7711 (mp0) cc_final: 0.7406 (mp0) REVERT: F 564 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7609 (t) REVERT: F 573 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 585 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5639 (pt0) REVERT: F 596 ARG cc_start: 0.7503 (mtp85) cc_final: 0.6975 (mtp85) REVERT: F 641 LEU cc_start: 0.6270 (mm) cc_final: 0.5729 (mm) REVERT: F 738 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7336 (tm-30) outliers start: 93 outliers final: 67 residues processed: 758 average time/residue: 0.2616 time to fit residues: 301.9753 Evaluate side-chains 776 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 698 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 430 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 762 THR Chi-restraints excluded: chain F residue 765 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 377 optimal weight: 10.0000 chunk 408 optimal weight: 0.5980 chunk 407 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 179 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 135 GLN B 356 ASN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN D 301 ASN E 233 ASN E 301 ASN F 44 HIS F 301 ASN F 304 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.169985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133896 restraints weight = 48964.525| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.24 r_work: 0.3434 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34688 Z= 0.212 Angle : 0.630 9.548 47036 Z= 0.321 Chirality : 0.047 0.274 5455 Planarity : 0.005 0.091 6062 Dihedral : 9.261 170.161 4942 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 2.76 % Allowed : 14.53 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4360 helix: 0.81 (0.13), residues: 1738 sheet: -0.65 (0.21), residues: 617 loop : -0.62 (0.15), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 434 TYR 0.017 0.002 TYR F 444 PHE 0.020 0.002 PHE E 217 TRP 0.006 0.001 TRP E 515 HIS 0.008 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00513 (34687) covalent geometry : angle 0.63018 (47036) hydrogen bonds : bond 0.04080 ( 1424) hydrogen bonds : angle 4.64548 ( 3921) Misc. bond : bond 0.00296 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 719 time to evaluate : 1.339 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 47 GLU cc_start: 0.7668 (pm20) cc_final: 0.7232 (pm20) REVERT: A 276 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8270 (p) REVERT: A 304 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7298 (m110) REVERT: A 329 ASP cc_start: 0.8312 (t70) cc_final: 0.7953 (t0) REVERT: A 695 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7693 (tttt) REVERT: A 711 GLU cc_start: 0.7745 (tp30) cc_final: 0.7461 (tp30) REVERT: A 715 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8118 (mtp85) REVERT: B 71 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7330 (m) REVERT: B 252 LYS cc_start: 0.8515 (tptp) cc_final: 0.8240 (tptt) REVERT: B 263 ILE cc_start: 0.8915 (tp) cc_final: 0.8654 (tp) REVERT: B 322 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 417 ASP cc_start: 0.8484 (m-30) cc_final: 0.8265 (m-30) REVERT: B 562 SER cc_start: 0.8255 (p) cc_final: 0.7937 (p) REVERT: B 714 ASP cc_start: 0.8439 (m-30) cc_final: 0.8232 (m-30) REVERT: C 162 MET cc_start: 0.7015 (mtt) cc_final: 0.6795 (mtt) REVERT: C 377 MET cc_start: 0.8187 (mtp) cc_final: 0.7758 (mtp) REVERT: C 663 ASP cc_start: 0.7810 (p0) cc_final: 0.7573 (p0) REVERT: C 671 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8240 (ptm-80) REVERT: C 742 VAL cc_start: 0.6566 (OUTLIER) cc_final: 0.6318 (t) REVERT: C 755 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8083 (ttmm) REVERT: D 109 ILE cc_start: 0.8048 (mt) cc_final: 0.7761 (mt) REVERT: D 128 LYS cc_start: 0.7796 (tttt) cc_final: 0.7560 (tttt) REVERT: D 231 GLN cc_start: 0.8235 (mp-120) cc_final: 0.7557 (mp-120) REVERT: D 363 GLU cc_start: 0.7232 (mp0) cc_final: 0.6728 (mp0) REVERT: D 534 LEU cc_start: 0.8384 (tp) cc_final: 0.8084 (tp) REVERT: D 589 LYS cc_start: 0.8651 (tttt) cc_final: 0.8433 (tttt) REVERT: D 664 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7802 (mm-30) REVERT: D 699 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8547 (mtpt) REVERT: D 704 GLU cc_start: 0.7137 (mp0) cc_final: 0.6654 (mp0) REVERT: D 708 ASP cc_start: 0.7684 (p0) cc_final: 0.7419 (p0) REVERT: E 37 ARG cc_start: 0.6933 (mtp85) cc_final: 0.5387 (tpt90) REVERT: E 107 ASN cc_start: 0.7666 (t0) cc_final: 0.7302 (t0) REVERT: E 177 ASP cc_start: 0.5933 (m-30) cc_final: 0.5663 (m-30) REVERT: E 269 THR cc_start: 0.7921 (p) cc_final: 0.6884 (m) REVERT: E 407 GLN cc_start: 0.7926 (mt0) cc_final: 0.7373 (mp10) REVERT: E 419 ARG cc_start: 0.7623 (mtm180) cc_final: 0.6870 (mtm-85) REVERT: E 448 LYS cc_start: 0.8121 (pptt) cc_final: 0.7806 (pptt) REVERT: E 495 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5676 (pmm) REVERT: E 530 GLU cc_start: 0.7551 (tp30) cc_final: 0.7043 (tp30) REVERT: E 664 GLU cc_start: 0.6736 (mm-30) cc_final: 0.5482 (tp30) REVERT: E 730 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6506 (tm-30) REVERT: F 162 MET cc_start: 0.6798 (mmm) cc_final: 0.6346 (mmm) REVERT: F 258 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7842 (mmmm) REVERT: F 262 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6939 (mt-10) REVERT: F 280 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6900 (ttm170) REVERT: F 375 ASP cc_start: 0.7066 (p0) cc_final: 0.6766 (p0) REVERT: F 399 LEU cc_start: 0.8326 (mp) cc_final: 0.8088 (mm) REVERT: F 417 ASP cc_start: 0.8426 (t70) cc_final: 0.8117 (t0) REVERT: F 419 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7421 (mtm180) REVERT: F 430 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6072 (ptp) REVERT: F 497 ASP cc_start: 0.7824 (m-30) cc_final: 0.6603 (t0) REVERT: F 499 ARG cc_start: 0.8129 (mpp-170) cc_final: 0.7927 (mpp-170) REVERT: F 523 GLU cc_start: 0.7715 (mp0) cc_final: 0.7396 (mp0) REVERT: F 564 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7687 (t) REVERT: F 573 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7577 (tm-30) REVERT: F 585 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5788 (pt0) REVERT: F 596 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6997 (mtp85) REVERT: F 717 GLU cc_start: 0.8502 (tp30) cc_final: 0.7238 (tp30) REVERT: F 730 GLU cc_start: 0.7987 (tt0) cc_final: 0.7761 (mt-10) REVERT: F 738 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7281 (tm-30) REVERT: F 770 GLU cc_start: 0.7159 (tp30) cc_final: 0.6694 (tp30) outliers start: 102 outliers final: 79 residues processed: 766 average time/residue: 0.2591 time to fit residues: 301.9092 Evaluate side-chains 788 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 701 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 430 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 762 THR Chi-restraints excluded: chain F residue 765 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 203 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 237 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 351 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 356 ASN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 338 GLN C 353 ASN D 301 ASN E 233 ASN F 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.172221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136236 restraints weight = 48767.619| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34688 Z= 0.120 Angle : 0.584 12.037 47036 Z= 0.295 Chirality : 0.044 0.198 5455 Planarity : 0.005 0.078 6062 Dihedral : 9.057 168.574 4942 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 2.14 % Allowed : 15.35 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4360 helix: 1.01 (0.13), residues: 1741 sheet: -0.55 (0.21), residues: 594 loop : -0.51 (0.15), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 603 TYR 0.016 0.001 TYR D 768 PHE 0.018 0.001 PHE F 578 TRP 0.006 0.001 TRP E 515 HIS 0.009 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00281 (34687) covalent geometry : angle 0.58428 (47036) hydrogen bonds : bond 0.03439 ( 1424) hydrogen bonds : angle 4.48112 ( 3921) Misc. bond : bond 0.00156 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 711 time to evaluate : 0.833 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 47 GLU cc_start: 0.7691 (pm20) cc_final: 0.7234 (pm20) REVERT: A 304 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7187 (m110) REVERT: A 329 ASP cc_start: 0.8283 (t70) cc_final: 0.7927 (t0) REVERT: A 695 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7674 (tttt) REVERT: A 711 GLU cc_start: 0.7827 (tp30) cc_final: 0.7547 (tp30) REVERT: A 715 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8016 (mtp85) REVERT: A 744 LYS cc_start: 0.8578 (ptmt) cc_final: 0.8252 (ptpp) REVERT: A 751 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: B 71 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7377 (m) REVERT: B 252 LYS cc_start: 0.8496 (tptp) cc_final: 0.8239 (tptt) REVERT: B 263 ILE cc_start: 0.8884 (tp) cc_final: 0.8625 (tp) REVERT: B 322 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 562 SER cc_start: 0.8153 (p) cc_final: 0.7822 (p) REVERT: B 714 ASP cc_start: 0.8419 (m-30) cc_final: 0.8193 (m-30) REVERT: C 162 MET cc_start: 0.7065 (mtt) cc_final: 0.6836 (mtt) REVERT: C 210 TYR cc_start: 0.5301 (m-80) cc_final: 0.5064 (m-10) REVERT: C 377 MET cc_start: 0.8140 (mtp) cc_final: 0.7686 (mtp) REVERT: C 453 VAL cc_start: 0.8495 (p) cc_final: 0.8211 (m) REVERT: C 463 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7669 (mm-30) REVERT: C 551 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7661 (mmtt) REVERT: C 553 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8365 (t) REVERT: C 671 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8232 (ptm-80) REVERT: C 742 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6252 (t) REVERT: C 755 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8082 (ttmm) REVERT: D 109 ILE cc_start: 0.8016 (mt) cc_final: 0.7760 (mt) REVERT: D 128 LYS cc_start: 0.7801 (tttt) cc_final: 0.7561 (tttt) REVERT: D 218 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6282 (mtp85) REVERT: D 231 GLN cc_start: 0.8226 (mp-120) cc_final: 0.7616 (mp-120) REVERT: D 363 GLU cc_start: 0.7169 (mp0) cc_final: 0.6662 (mp0) REVERT: D 495 MET cc_start: 0.8271 (ttm) cc_final: 0.8029 (ttp) REVERT: D 589 LYS cc_start: 0.8669 (tttt) cc_final: 0.8451 (tttt) REVERT: D 664 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7859 (mm-30) REVERT: D 699 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8546 (mtpt) REVERT: D 704 GLU cc_start: 0.7143 (mp0) cc_final: 0.6636 (mp0) REVERT: E 37 ARG cc_start: 0.6835 (mtp85) cc_final: 0.5404 (tpt90) REVERT: E 107 ASN cc_start: 0.7733 (t0) cc_final: 0.7339 (t0) REVERT: E 269 THR cc_start: 0.7958 (p) cc_final: 0.6854 (m) REVERT: E 297 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7927 (mmm160) REVERT: E 407 GLN cc_start: 0.7831 (mt0) cc_final: 0.7496 (mp10) REVERT: E 419 ARG cc_start: 0.7524 (mtm180) cc_final: 0.6795 (mtm-85) REVERT: E 436 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5178 (t) REVERT: E 448 LYS cc_start: 0.8099 (pptt) cc_final: 0.7778 (pptt) REVERT: E 495 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5459 (pmm) REVERT: E 530 GLU cc_start: 0.7571 (tp30) cc_final: 0.7028 (tp30) REVERT: E 664 GLU cc_start: 0.6755 (mm-30) cc_final: 0.5582 (tp30) REVERT: E 730 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6576 (tm-30) REVERT: F 162 MET cc_start: 0.6694 (mmm) cc_final: 0.6240 (mmm) REVERT: F 258 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7774 (mmmm) REVERT: F 262 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6980 (mt-10) REVERT: F 280 ARG cc_start: 0.7119 (ttm170) cc_final: 0.6818 (ttm170) REVERT: F 292 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8076 (mtmm) REVERT: F 365 ARG cc_start: 0.5144 (ttm110) cc_final: 0.4928 (ttm170) REVERT: F 375 ASP cc_start: 0.7100 (p0) cc_final: 0.6819 (p0) REVERT: F 399 LEU cc_start: 0.8270 (mp) cc_final: 0.8050 (mm) REVERT: F 417 ASP cc_start: 0.8391 (t70) cc_final: 0.8099 (t0) REVERT: F 419 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7407 (mtm180) REVERT: F 430 MET cc_start: 0.6384 (mpp) cc_final: 0.6068 (ptp) REVERT: F 490 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6612 (t0) REVERT: F 497 ASP cc_start: 0.7778 (m-30) cc_final: 0.6561 (t0) REVERT: F 499 ARG cc_start: 0.8158 (mpp-170) cc_final: 0.7931 (mpp-170) REVERT: F 503 MET cc_start: 0.8182 (mmm) cc_final: 0.7977 (mmm) REVERT: F 523 GLU cc_start: 0.7739 (mp0) cc_final: 0.7429 (mp0) REVERT: F 564 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7638 (t) REVERT: F 573 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7514 (tm-30) REVERT: F 585 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5571 (pt0) REVERT: F 596 ARG cc_start: 0.7564 (mtp85) cc_final: 0.6974 (mtp85) REVERT: F 717 GLU cc_start: 0.8432 (tp30) cc_final: 0.7421 (tp30) REVERT: F 738 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7264 (tm-30) outliers start: 79 outliers final: 54 residues processed: 750 average time/residue: 0.2460 time to fit residues: 281.6703 Evaluate side-chains 762 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 697 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 374 MET Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 585 GLU Chi-restraints excluded: chain F residue 762 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 46 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 243 optimal weight: 0.6980 chunk 238 optimal weight: 0.6980 chunk 329 optimal weight: 3.9990 chunk 369 optimal weight: 0.9980 chunk 296 optimal weight: 20.0000 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 135 GLN B 356 ASN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN D 301 ASN E 233 ASN E 301 ASN F 301 ASN F 304 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136260 restraints weight = 48905.019| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.25 r_work: 0.3470 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34688 Z= 0.129 Angle : 0.592 11.747 47036 Z= 0.298 Chirality : 0.044 0.362 5455 Planarity : 0.005 0.072 6062 Dihedral : 8.996 170.614 4942 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 2.14 % Allowed : 15.37 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4360 helix: 1.05 (0.13), residues: 1740 sheet: -0.53 (0.21), residues: 596 loop : -0.47 (0.15), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 280 TYR 0.016 0.001 TYR D 768 PHE 0.019 0.001 PHE F 578 TRP 0.006 0.001 TRP E 515 HIS 0.012 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00308 (34687) covalent geometry : angle 0.59171 (47036) hydrogen bonds : bond 0.03483 ( 1424) hydrogen bonds : angle 4.45442 ( 3921) Misc. bond : bond 0.00176 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 709 time to evaluate : 1.366 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 47 GLU cc_start: 0.7689 (pm20) cc_final: 0.7227 (pm20) REVERT: A 276 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 304 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7117 (m110) REVERT: A 329 ASP cc_start: 0.8294 (t70) cc_final: 0.7948 (t0) REVERT: A 514 TYR cc_start: 0.8797 (m-80) cc_final: 0.8482 (m-80) REVERT: A 695 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7673 (tttt) REVERT: A 711 GLU cc_start: 0.7744 (tp30) cc_final: 0.7459 (tp30) REVERT: A 715 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8018 (mtp85) REVERT: A 744 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8242 (ptpp) REVERT: A 751 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: B 71 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7361 (m) REVERT: B 252 LYS cc_start: 0.8512 (tptp) cc_final: 0.8250 (tptt) REVERT: B 263 ILE cc_start: 0.8894 (tp) cc_final: 0.8641 (tp) REVERT: B 322 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 562 SER cc_start: 0.8157 (p) cc_final: 0.7815 (p) REVERT: B 714 ASP cc_start: 0.8445 (m-30) cc_final: 0.8239 (m-30) REVERT: C 162 MET cc_start: 0.7084 (mtt) cc_final: 0.6833 (mtt) REVERT: C 210 TYR cc_start: 0.5394 (m-80) cc_final: 0.5144 (m-80) REVERT: C 332 ASN cc_start: 0.7995 (m-40) cc_final: 0.7542 (m110) REVERT: C 377 MET cc_start: 0.8150 (mtp) cc_final: 0.7704 (mtp) REVERT: C 453 VAL cc_start: 0.8510 (p) cc_final: 0.8199 (m) REVERT: C 537 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 671 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8255 (ptm-80) REVERT: C 742 VAL cc_start: 0.6522 (OUTLIER) cc_final: 0.6251 (t) REVERT: C 755 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8090 (ttmm) REVERT: C 772 PHE cc_start: 0.8506 (t80) cc_final: 0.8008 (t80) REVERT: D 109 ILE cc_start: 0.7930 (mt) cc_final: 0.7654 (mt) REVERT: D 128 LYS cc_start: 0.7798 (tttt) cc_final: 0.7571 (tttt) REVERT: D 218 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6321 (mtp85) REVERT: D 231 GLN cc_start: 0.8205 (mp-120) cc_final: 0.7593 (mp-120) REVERT: D 363 GLU cc_start: 0.7166 (mp0) cc_final: 0.6674 (mp0) REVERT: D 589 LYS cc_start: 0.8653 (tttt) cc_final: 0.8442 (tttt) REVERT: D 664 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 704 GLU cc_start: 0.7153 (mp0) cc_final: 0.6650 (mp0) REVERT: D 709 LEU cc_start: 0.7512 (mt) cc_final: 0.7303 (mt) REVERT: D 711 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7270 (tm-30) REVERT: E 37 ARG cc_start: 0.6798 (mtp85) cc_final: 0.5336 (tpt90) REVERT: E 269 THR cc_start: 0.8017 (p) cc_final: 0.6893 (m) REVERT: E 297 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7923 (mmm160) REVERT: E 407 GLN cc_start: 0.7772 (mt0) cc_final: 0.7558 (mt0) REVERT: E 419 ARG cc_start: 0.7485 (mtm180) cc_final: 0.6772 (mtm-85) REVERT: E 436 VAL cc_start: 0.6080 (OUTLIER) cc_final: 0.5130 (t) REVERT: E 448 LYS cc_start: 0.8107 (pptt) cc_final: 0.7786 (pptt) REVERT: E 495 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5281 (pmm) REVERT: E 530 GLU cc_start: 0.7562 (tp30) cc_final: 0.7018 (tp30) REVERT: E 664 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5605 (tp30) REVERT: E 730 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6539 (tm-30) REVERT: F 162 MET cc_start: 0.6792 (mmm) cc_final: 0.6331 (mmm) REVERT: F 280 ARG cc_start: 0.7162 (ttm170) cc_final: 0.6812 (ttm170) REVERT: F 292 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8355 (mtmm) REVERT: F 365 ARG cc_start: 0.5181 (ttm110) cc_final: 0.4965 (ttm170) REVERT: F 375 ASP cc_start: 0.7137 (p0) cc_final: 0.6884 (p0) REVERT: F 417 ASP cc_start: 0.8364 (t70) cc_final: 0.8077 (t0) REVERT: F 419 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7432 (mtm180) REVERT: F 490 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6657 (t0) REVERT: F 497 ASP cc_start: 0.7854 (m-30) cc_final: 0.6678 (t0) REVERT: F 499 ARG cc_start: 0.8129 (mpp-170) cc_final: 0.7906 (mpp-170) REVERT: F 513 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8398 (p) REVERT: F 523 GLU cc_start: 0.7724 (mp0) cc_final: 0.7420 (mp0) REVERT: F 564 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (t) REVERT: F 573 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 596 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6927 (mtp85) REVERT: F 643 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6838 (mm-30) REVERT: F 738 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7191 (tm-30) outliers start: 79 outliers final: 61 residues processed: 748 average time/residue: 0.2556 time to fit residues: 292.3203 Evaluate side-chains 771 residues out of total 3695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 699 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 390 ASN Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 762 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 37 optimal weight: 0.6980 chunk 351 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 253 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 135 GLN A 435 HIS B 356 ASN B 407 GLN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN E 107 ASN E 233 ASN E 301 ASN F 301 ASN F 304 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.172839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136807 restraints weight = 48630.450| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.23 r_work: 0.3481 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34688 Z= 0.119 Angle : 0.589 13.358 47036 Z= 0.296 Chirality : 0.044 0.357 5455 Planarity : 0.005 0.070 6062 Dihedral : 8.930 170.846 4942 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 2.00 % Allowed : 15.56 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4360 helix: 1.10 (0.13), residues: 1747 sheet: -0.46 (0.21), residues: 592 loop : -0.42 (0.15), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 280 TYR 0.016 0.001 TYR D 768 PHE 0.020 0.001 PHE F 578 TRP 0.006 0.001 TRP E 515 HIS 0.010 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00279 (34687) covalent geometry : angle 0.58907 (47036) hydrogen bonds : bond 0.03380 ( 1424) hydrogen bonds : angle 4.41394 ( 3921) Misc. bond : bond 0.00167 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10869.39 seconds wall clock time: 186 minutes 8.17 seconds (11168.17 seconds total)