Starting phenix.real_space_refine on Wed Jul 30 09:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0g_37978/07_2025/8x0g_37978.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 7774 2.51 5 N 2006 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12129 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6022 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 32, 'TRANS': 732} Chain breaks: 2 Chain: "B" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6022 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 32, 'TRANS': 732} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'QUS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'QUS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 9.49, per 1000 atoms: 0.78 Number of scatterers: 12129 At special positions: 0 Unit cell: (105.84, 79.8, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2235 8.00 N 2006 7.00 C 7774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.05 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.04 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 2.1 seconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 49.9% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 4.057A pdb=" N GLU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.784A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.766A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 removed outlier: 4.010A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 Processing helix chain 'A' and resid 253 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.628A pdb=" N ALA A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.989A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.685A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.552A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.825A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 removed outlier: 3.584A pdb=" N THR A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.526A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 614 through 632 removed outlier: 3.513A pdb=" N CYS A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 646 through 672 Proline residue: A 655 - end of helix removed outlier: 3.808A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.646A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 762 removed outlier: 4.034A pdb=" N ALA A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Proline residue: A 743 - end of helix removed outlier: 3.795A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.961A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 782 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) Proline residue: A 790 - end of helix removed outlier: 3.513A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.565A pdb=" N MET A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 removed outlier: 3.615A pdb=" N VAL A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.772A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.617A pdb=" N ARG B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.556A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.563A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.687A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.921A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.670A pdb=" N THR B 563 " --> pdb=" O ASP B 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.841A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 636 removed outlier: 4.944A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 672 Proline residue: B 655 - end of helix removed outlier: 3.851A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 691 No H-bonds generated for 'chain 'B' and resid 689 through 691' Processing helix chain 'B' and resid 692 through 715 removed outlier: 4.180A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 709 " --> pdb=" O LEU B 705 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 762 removed outlier: 3.511A pdb=" N VAL B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix removed outlier: 3.712A pdb=" N TYR B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 768 No H-bonds generated for 'chain 'B' and resid 766 through 768' Processing helix chain 'B' and resid 769 through 778 removed outlier: 3.514A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 794 removed outlier: 4.172A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix removed outlier: 3.632A pdb=" N GLY B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 827 removed outlier: 3.637A pdb=" N THR B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Proline residue: B 820 - end of helix removed outlier: 3.701A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.303A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN A 169 " --> pdb=" O MET A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 7.756A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.627A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 524 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.265A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE B 36 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 146 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 38 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN B 169 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.099A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 219 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.709A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 520 through 523 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AB7, first strand: chain 'B' and resid 719 through 722 520 hydrogen bonds defined for protein. 1509 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: 4.93 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2255 1.33 - 1.46: 4146 1.46 - 1.58: 5809 1.58 - 1.71: 0 1.71 - 1.84: 164 Bond restraints: 12374 Sorted by residual: bond pdb=" C SER B 654 " pdb=" N PRO B 655 " ideal model delta sigma weight residual 1.331 1.353 -0.022 7.90e-03 1.60e+04 7.66e+00 bond pdb=" C SER A 654 " pdb=" N PRO A 655 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.40e+00 bond pdb=" CA SER B 462 " pdb=" CB SER B 462 " ideal model delta sigma weight residual 1.537 1.504 0.033 1.38e-02 5.25e+03 5.70e+00 bond pdb=" CA ALA A 637 " pdb=" CB ALA A 637 " ideal model delta sigma weight residual 1.538 1.511 0.027 1.22e-02 6.72e+03 4.96e+00 bond pdb=" CA SER A 462 " pdb=" CB SER A 462 " ideal model delta sigma weight residual 1.537 1.507 0.031 1.38e-02 5.25e+03 4.92e+00 ... (remaining 12369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 16286 1.99 - 3.98: 465 3.98 - 5.97: 10 5.97 - 7.96: 6 7.96 - 9.95: 3 Bond angle restraints: 16770 Sorted by residual: angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 122.72 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N SER B 809 " pdb=" CA SER B 809 " pdb=" C SER B 809 " ideal model delta sigma weight residual 112.38 108.37 4.01 1.22e+00 6.72e-01 1.08e+01 angle pdb=" C03 QUS A 902 " pdb=" N14 QUS A 902 " pdb=" O20 QUS A 902 " ideal model delta sigma weight residual 112.77 122.58 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O PHE B 370 " pdb=" C PHE B 370 " pdb=" N PRO B 371 " ideal model delta sigma weight residual 121.71 119.75 1.96 6.40e-01 2.44e+00 9.35e+00 angle pdb=" CA CYS B 365 " pdb=" C CYS B 365 " pdb=" O CYS B 365 " ideal model delta sigma weight residual 121.31 118.28 3.03 1.07e+00 8.73e-01 8.04e+00 ... (remaining 16765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 6670 21.21 - 42.42: 647 42.42 - 63.63: 119 63.63 - 84.84: 16 84.84 - 106.05: 18 Dihedral angle restraints: 7470 sinusoidal: 3016 harmonic: 4454 Sorted by residual: dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual 93.00 174.44 -81.44 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -159.10 73.10 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 99 " pdb=" CB CYS A 99 " ideal model delta sinusoidal sigma weight residual -86.00 -25.21 -60.79 1 1.00e+01 1.00e-02 4.91e+01 ... (remaining 7467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1276 0.064 - 0.129: 581 0.129 - 0.193: 27 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 1886 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PRO A 580 " pdb=" N PRO A 580 " pdb=" C PRO A 580 " pdb=" CB PRO A 580 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1883 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 362 " 0.244 9.50e-02 1.11e+02 1.09e-01 7.54e+00 pdb=" NE ARG B 362 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 362 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 362 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 362 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 114 " 0.159 9.50e-02 1.11e+02 7.15e-02 3.68e+00 pdb=" NE ARG A 114 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 114 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 114 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 114 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 403 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ALA A 403 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA A 403 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 404 " 0.009 2.00e-02 2.50e+03 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2399 2.78 - 3.31: 12270 3.31 - 3.84: 20397 3.84 - 4.37: 24359 4.37 - 4.90: 40660 Nonbonded interactions: 100085 Sorted by model distance: nonbonded pdb=" NH2 ARG A 362 " pdb=" O THR A 389 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A 26 " pdb=" O ARG A 55 " model vdw 2.283 3.120 nonbonded pdb=" O SER B 529 " pdb=" OG SER B 529 " model vdw 2.291 3.040 nonbonded pdb=" N TYR B 213 " pdb=" O SER B 509 " model vdw 2.299 3.120 ... (remaining 100080 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.460 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.040 12396 Z= 0.425 Angle : 0.869 9.948 16816 Z= 0.562 Chirality : 0.061 0.322 1886 Planarity : 0.006 0.109 2112 Dihedral : 17.332 106.051 4554 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.91 % Favored : 91.70 % Rotamer: Outliers : 0.76 % Allowed : 21.33 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1518 helix: -0.42 (0.19), residues: 696 sheet: -1.03 (0.41), residues: 146 loop : -1.86 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 336 HIS 0.009 0.002 HIS A 30 PHE 0.024 0.003 PHE A 112 TYR 0.021 0.003 TYR B 172 ARG 0.017 0.002 ARG B 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 2) link_NAG-ASN : angle 3.30266 ( 6) hydrogen bonds : bond 0.18015 ( 520) hydrogen bonds : angle 6.52896 ( 1509) SS BOND : bond 0.00756 ( 20) SS BOND : angle 1.41795 ( 40) covalent geometry : bond 0.00654 (12374) covalent geometry : angle 0.86547 (16770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 546 GLU cc_start: 0.8386 (tp30) cc_final: 0.8166 (tp30) REVERT: A 711 LEU cc_start: 0.7358 (mt) cc_final: 0.7129 (mp) REVERT: B 277 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 374 ASN cc_start: 0.7334 (t0) cc_final: 0.6577 (t0) REVERT: B 508 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6977 (mpp80) outliers start: 10 outliers final: 2 residues processed: 157 average time/residue: 1.2188 time to fit residues: 208.7483 Evaluate side-chains 138 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 277 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 360 GLN B 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106092 restraints weight = 16593.949| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.74 r_work: 0.3263 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12396 Z= 0.193 Angle : 0.637 7.016 16816 Z= 0.324 Chirality : 0.045 0.213 1886 Planarity : 0.004 0.041 2112 Dihedral : 10.002 78.153 1727 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.03 % Allowed : 23.30 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1518 helix: 0.31 (0.20), residues: 698 sheet: -1.04 (0.40), residues: 153 loop : -1.76 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 359 HIS 0.004 0.001 HIS A 218 PHE 0.013 0.001 PHE B 337 TYR 0.014 0.001 TYR B 645 ARG 0.009 0.000 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 2) link_NAG-ASN : angle 2.98577 ( 6) hydrogen bonds : bond 0.05556 ( 520) hydrogen bonds : angle 4.67257 ( 1509) SS BOND : bond 0.00641 ( 20) SS BOND : angle 1.63991 ( 40) covalent geometry : bond 0.00444 (12374) covalent geometry : angle 0.63057 (16770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: A 546 GLU cc_start: 0.8292 (tp30) cc_final: 0.8068 (tp30) REVERT: A 720 MET cc_start: 0.7933 (ppp) cc_final: 0.7455 (ppp) REVERT: B 277 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8226 (t80) REVERT: B 335 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8183 (mppt) REVERT: B 374 ASN cc_start: 0.7980 (t0) cc_final: 0.7568 (t0) REVERT: B 657 MET cc_start: 0.6447 (ppp) cc_final: 0.6127 (ppp) REVERT: B 720 MET cc_start: 0.6444 (tmm) cc_final: 0.6242 (tmm) REVERT: B 817 MET cc_start: 0.7334 (mmm) cc_final: 0.6416 (tmm) outliers start: 40 outliers final: 14 residues processed: 163 average time/residue: 1.1002 time to fit residues: 197.3492 Evaluate side-chains 149 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 625 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.166654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107617 restraints weight = 16618.261| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.77 r_work: 0.3286 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12396 Z= 0.137 Angle : 0.579 7.533 16816 Z= 0.289 Chirality : 0.043 0.235 1886 Planarity : 0.004 0.049 2112 Dihedral : 7.353 59.478 1727 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.46 % Allowed : 22.77 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1518 helix: 0.54 (0.20), residues: 700 sheet: -0.85 (0.42), residues: 146 loop : -1.67 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 354 HIS 0.003 0.000 HIS A 218 PHE 0.013 0.001 PHE A 698 TYR 0.009 0.001 TYR B 547 ARG 0.010 0.000 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 2) link_NAG-ASN : angle 3.02780 ( 6) hydrogen bonds : bond 0.04485 ( 520) hydrogen bonds : angle 4.36753 ( 1509) SS BOND : bond 0.00383 ( 20) SS BOND : angle 1.02853 ( 40) covalent geometry : bond 0.00311 (12374) covalent geometry : angle 0.57428 (16770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 222 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8839 (t0) REVERT: A 546 GLU cc_start: 0.8287 (tp30) cc_final: 0.8071 (tp30) REVERT: A 720 MET cc_start: 0.7963 (ppp) cc_final: 0.7394 (ppp) REVERT: B 277 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 335 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8187 (mppt) REVERT: B 374 ASN cc_start: 0.8117 (t0) cc_final: 0.7822 (t0) REVERT: B 547 TYR cc_start: 0.8226 (m-10) cc_final: 0.7995 (m-10) REVERT: B 657 MET cc_start: 0.6786 (ppp) cc_final: 0.6495 (ppp) REVERT: B 720 MET cc_start: 0.6639 (tmm) cc_final: 0.6336 (tmm) REVERT: B 802 MET cc_start: 0.7636 (tpt) cc_final: 0.7436 (tpt) REVERT: B 817 MET cc_start: 0.7172 (mmm) cc_final: 0.6442 (tmm) outliers start: 59 outliers final: 23 residues processed: 177 average time/residue: 1.2857 time to fit residues: 250.6823 Evaluate side-chains 157 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 0.0030 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.167284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108517 restraints weight = 16482.057| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.78 r_work: 0.3300 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12396 Z= 0.125 Angle : 0.584 8.123 16816 Z= 0.289 Chirality : 0.043 0.233 1886 Planarity : 0.004 0.053 2112 Dihedral : 6.349 59.437 1725 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.31 % Allowed : 23.45 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1518 helix: 0.67 (0.20), residues: 698 sheet: -0.99 (0.41), residues: 156 loop : -1.63 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 354 HIS 0.003 0.000 HIS A 218 PHE 0.011 0.001 PHE A 698 TYR 0.018 0.001 TYR B 645 ARG 0.012 0.000 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 2) link_NAG-ASN : angle 3.12239 ( 6) hydrogen bonds : bond 0.04090 ( 520) hydrogen bonds : angle 4.25484 ( 1509) SS BOND : bond 0.00494 ( 20) SS BOND : angle 1.87523 ( 40) covalent geometry : bond 0.00289 (12374) covalent geometry : angle 0.57411 (16770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 372 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6526 (mt0) REVERT: A 546 GLU cc_start: 0.8275 (tp30) cc_final: 0.8074 (tp30) REVERT: A 720 MET cc_start: 0.8012 (ppp) cc_final: 0.7423 (ppp) REVERT: B 115 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8134 (t70) REVERT: B 374 ASN cc_start: 0.8210 (t0) cc_final: 0.7984 (t0) REVERT: B 645 TYR cc_start: 0.7601 (p90) cc_final: 0.7384 (p90) REVERT: B 657 MET cc_start: 0.6923 (ppp) cc_final: 0.6597 (ppp) REVERT: B 720 MET cc_start: 0.6555 (tmm) cc_final: 0.6192 (tmm) REVERT: B 817 MET cc_start: 0.7187 (mmm) cc_final: 0.6587 (tmm) outliers start: 57 outliers final: 25 residues processed: 174 average time/residue: 1.1173 time to fit residues: 214.2213 Evaluate side-chains 158 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 625 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 667 ASN B 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106434 restraints weight = 16611.864| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.79 r_work: 0.3271 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12396 Z= 0.172 Angle : 0.613 8.888 16816 Z= 0.302 Chirality : 0.043 0.238 1886 Planarity : 0.004 0.060 2112 Dihedral : 6.064 58.510 1723 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.46 % Allowed : 23.60 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1518 helix: 0.66 (0.20), residues: 695 sheet: -0.82 (0.42), residues: 151 loop : -1.66 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 354 HIS 0.004 0.001 HIS A 218 PHE 0.014 0.001 PHE B 337 TYR 0.015 0.001 TYR B 645 ARG 0.014 0.000 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 2) link_NAG-ASN : angle 5.85596 ( 6) hydrogen bonds : bond 0.04280 ( 520) hydrogen bonds : angle 4.25739 ( 1509) SS BOND : bond 0.00459 ( 20) SS BOND : angle 1.61840 ( 40) covalent geometry : bond 0.00405 (12374) covalent geometry : angle 0.59885 (16770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5501 (tpt) REVERT: A 433 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7379 (t0) REVERT: A 568 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5848 (pp) REVERT: A 618 CYS cc_start: 0.7577 (m) cc_final: 0.6214 (p) REVERT: A 720 MET cc_start: 0.8033 (ppp) cc_final: 0.7409 (ppp) REVERT: B 657 MET cc_start: 0.6934 (ppp) cc_final: 0.6555 (ppp) REVERT: B 720 MET cc_start: 0.6752 (tmm) cc_final: 0.6384 (tmm) REVERT: B 817 MET cc_start: 0.7314 (tmm) cc_final: 0.6701 (tmm) outliers start: 59 outliers final: 32 residues processed: 171 average time/residue: 1.4518 time to fit residues: 272.9360 Evaluate side-chains 162 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.162830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103214 restraints weight = 16897.478| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.75 r_work: 0.3213 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 12396 Z= 0.310 Angle : 0.702 10.503 16816 Z= 0.353 Chirality : 0.048 0.312 1886 Planarity : 0.005 0.058 2112 Dihedral : 6.313 57.150 1723 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 5.37 % Allowed : 23.60 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1518 helix: 0.49 (0.20), residues: 698 sheet: -1.20 (0.41), residues: 155 loop : -1.80 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 100 HIS 0.005 0.001 HIS A 218 PHE 0.020 0.002 PHE B 337 TYR 0.020 0.002 TYR B 377 ARG 0.015 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 2) link_NAG-ASN : angle 6.78813 ( 6) hydrogen bonds : bond 0.05060 ( 520) hydrogen bonds : angle 4.49368 ( 1509) SS BOND : bond 0.00634 ( 20) SS BOND : angle 1.90072 ( 40) covalent geometry : bond 0.00740 (12374) covalent geometry : angle 0.68498 (16770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 372 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6461 (mt0) REVERT: A 429 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5596 (tpt) REVERT: A 433 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 720 MET cc_start: 0.8031 (ppp) cc_final: 0.7406 (ppp) REVERT: B 657 MET cc_start: 0.6992 (ppp) cc_final: 0.6690 (ppp) REVERT: B 720 MET cc_start: 0.6734 (tmm) cc_final: 0.6353 (tmm) REVERT: B 817 MET cc_start: 0.7699 (tmm) cc_final: 0.6987 (tmm) outliers start: 71 outliers final: 39 residues processed: 175 average time/residue: 1.5368 time to fit residues: 298.1467 Evaluate side-chains 167 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 808 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.4980 chunk 90 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 108 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107141 restraints weight = 16681.796| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.80 r_work: 0.3277 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 12396 Z= 0.133 Angle : 0.636 11.847 16816 Z= 0.314 Chirality : 0.044 0.260 1886 Planarity : 0.004 0.072 2112 Dihedral : 6.050 58.050 1723 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.93 % Allowed : 25.64 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1518 helix: 0.67 (0.20), residues: 701 sheet: -0.92 (0.43), residues: 144 loop : -1.62 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.003 0.000 HIS A 218 PHE 0.018 0.001 PHE B 776 TYR 0.019 0.001 TYR B 645 ARG 0.017 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 2) link_NAG-ASN : angle 5.40604 ( 6) hydrogen bonds : bond 0.03992 ( 520) hydrogen bonds : angle 4.25653 ( 1509) SS BOND : bond 0.00378 ( 20) SS BOND : angle 2.66559 ( 40) covalent geometry : bond 0.00315 (12374) covalent geometry : angle 0.61499 (16770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8507 (tpp) REVERT: A 372 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6386 (mt0) REVERT: A 433 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7361 (t0) REVERT: A 541 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 618 CYS cc_start: 0.7604 (m) cc_final: 0.6260 (p) REVERT: A 720 MET cc_start: 0.8016 (ppp) cc_final: 0.7366 (ppp) REVERT: A 788 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 657 MET cc_start: 0.6935 (ppp) cc_final: 0.6573 (ppp) REVERT: B 720 MET cc_start: 0.6827 (tmm) cc_final: 0.6464 (tmm) REVERT: B 817 MET cc_start: 0.7667 (tmm) cc_final: 0.7020 (tmm) outliers start: 52 outliers final: 27 residues processed: 169 average time/residue: 1.1354 time to fit residues: 214.9474 Evaluate side-chains 159 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 93 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107035 restraints weight = 16779.065| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.78 r_work: 0.3274 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12396 Z= 0.146 Angle : 0.635 11.426 16816 Z= 0.312 Chirality : 0.043 0.264 1886 Planarity : 0.004 0.076 2112 Dihedral : 5.924 59.879 1723 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.93 % Allowed : 25.87 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1518 helix: 0.74 (0.20), residues: 696 sheet: -0.89 (0.43), residues: 144 loop : -1.61 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.004 0.001 HIS A 218 PHE 0.015 0.001 PHE A 776 TYR 0.011 0.001 TYR A 572 ARG 0.019 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 2) link_NAG-ASN : angle 4.87607 ( 6) hydrogen bonds : bond 0.03998 ( 520) hydrogen bonds : angle 4.24915 ( 1509) SS BOND : bond 0.00456 ( 20) SS BOND : angle 2.27930 ( 40) covalent geometry : bond 0.00348 (12374) covalent geometry : angle 0.61973 (16770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8508 (tpp) REVERT: A 372 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6394 (mt0) REVERT: A 433 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7463 (t0) REVERT: A 541 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 618 CYS cc_start: 0.7599 (m) cc_final: 0.6254 (p) REVERT: A 645 TYR cc_start: 0.5637 (OUTLIER) cc_final: 0.5008 (p90) REVERT: A 720 MET cc_start: 0.8083 (ppp) cc_final: 0.7437 (ppp) REVERT: B 657 MET cc_start: 0.6920 (ppp) cc_final: 0.6557 (ppp) REVERT: B 720 MET cc_start: 0.6834 (tmm) cc_final: 0.6464 (tmm) REVERT: B 817 MET cc_start: 0.7575 (tmm) cc_final: 0.7355 (tmm) outliers start: 52 outliers final: 32 residues processed: 168 average time/residue: 1.1703 time to fit residues: 217.6618 Evaluate side-chains 165 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 644 CYS Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106147 restraints weight = 16655.722| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.76 r_work: 0.3263 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12396 Z= 0.178 Angle : 0.640 10.048 16816 Z= 0.316 Chirality : 0.044 0.276 1886 Planarity : 0.004 0.082 2112 Dihedral : 5.909 59.962 1723 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.71 % Allowed : 26.25 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1518 helix: 0.73 (0.20), residues: 695 sheet: -1.02 (0.41), residues: 154 loop : -1.65 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 354 HIS 0.004 0.001 HIS A 218 PHE 0.014 0.001 PHE B 337 TYR 0.018 0.001 TYR B 645 ARG 0.019 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 2) link_NAG-ASN : angle 4.84480 ( 6) hydrogen bonds : bond 0.04178 ( 520) hydrogen bonds : angle 4.22207 ( 1509) SS BOND : bond 0.00469 ( 20) SS BOND : angle 2.04401 ( 40) covalent geometry : bond 0.00426 (12374) covalent geometry : angle 0.62599 (16770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8571 (tpp) REVERT: A 372 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: A 429 MET cc_start: 0.5470 (tpt) cc_final: 0.5269 (tpt) REVERT: A 433 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7472 (t0) REVERT: A 541 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: A 618 CYS cc_start: 0.7664 (m) cc_final: 0.6261 (p) REVERT: A 720 MET cc_start: 0.8072 (ppp) cc_final: 0.7586 (ppp) REVERT: B 657 MET cc_start: 0.6930 (ppp) cc_final: 0.6673 (ppp) REVERT: B 720 MET cc_start: 0.6830 (tmm) cc_final: 0.6460 (tmm) REVERT: B 817 MET cc_start: 0.7572 (tmm) cc_final: 0.7277 (tmm) outliers start: 49 outliers final: 31 residues processed: 162 average time/residue: 1.3140 time to fit residues: 234.1569 Evaluate side-chains 162 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107180 restraints weight = 16574.468| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.78 r_work: 0.3281 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12396 Z= 0.140 Angle : 0.633 10.092 16816 Z= 0.310 Chirality : 0.043 0.259 1886 Planarity : 0.004 0.086 2112 Dihedral : 5.817 58.823 1723 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.40 % Allowed : 26.70 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1518 helix: 0.76 (0.20), residues: 695 sheet: -0.85 (0.43), residues: 144 loop : -1.59 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE B 788 TYR 0.012 0.001 TYR A 572 ARG 0.020 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 2) link_NAG-ASN : angle 4.24196 ( 6) hydrogen bonds : bond 0.03891 ( 520) hydrogen bonds : angle 4.23200 ( 1509) SS BOND : bond 0.00394 ( 20) SS BOND : angle 1.89647 ( 40) covalent geometry : bond 0.00332 (12374) covalent geometry : angle 0.62199 (16770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: A 372 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6383 (mt0) REVERT: A 433 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7485 (t0) REVERT: A 541 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 618 CYS cc_start: 0.7650 (m) cc_final: 0.6269 (p) REVERT: A 645 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.5101 (p90) REVERT: A 720 MET cc_start: 0.8092 (ppp) cc_final: 0.7417 (ppp) REVERT: B 657 MET cc_start: 0.6940 (ppp) cc_final: 0.6685 (ppp) REVERT: B 720 MET cc_start: 0.6856 (tmm) cc_final: 0.6483 (tmm) REVERT: B 778 MET cc_start: 0.8485 (mmm) cc_final: 0.7672 (ttp) REVERT: B 817 MET cc_start: 0.7609 (tmm) cc_final: 0.7005 (tmm) outliers start: 45 outliers final: 29 residues processed: 162 average time/residue: 1.1202 time to fit residues: 199.3784 Evaluate side-chains 163 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 645 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 791 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 143 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.163753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103231 restraints weight = 16574.059| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.73 r_work: 0.3145 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12396 Z= 0.137 Angle : 0.636 12.899 16816 Z= 0.309 Chirality : 0.043 0.256 1886 Planarity : 0.004 0.086 2112 Dihedral : 5.652 57.430 1723 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.25 % Allowed : 26.85 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1518 helix: 0.80 (0.20), residues: 694 sheet: -1.03 (0.42), residues: 154 loop : -1.59 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE B 788 TYR 0.020 0.001 TYR B 645 ARG 0.021 0.001 ARG B 727 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 2) link_NAG-ASN : angle 3.89316 ( 6) hydrogen bonds : bond 0.03801 ( 520) hydrogen bonds : angle 4.15585 ( 1509) SS BOND : bond 0.00431 ( 20) SS BOND : angle 1.72193 ( 40) covalent geometry : bond 0.00328 (12374) covalent geometry : angle 0.62718 (16770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11116.24 seconds wall clock time: 196 minutes 34.37 seconds (11794.37 seconds total)