Starting phenix.real_space_refine on Wed Jul 30 09:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0e_37976/07_2025/8x0e_37976.cif" } resolution = 3.4 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= 0.003 sd= 0.075 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 7760 2.51 5 N 2006 2.21 5 O 2206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12086 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6016 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 32, 'TRANS': 732} Chain breaks: 2 Chain: "B" Number of atoms: 6016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6016 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 Time building chain proxies: 9.70, per 1000 atoms: 0.80 Number of scatterers: 12086 At special positions: 0 Unit cell: (170.13, 123.05, 160.5, 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 2206 8.00 N 2006 7.00 C 7760 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=2.06 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.04 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 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: 3.39 Conformation dependent library (CDL) restraints added in 1.8 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: 54 helices and 19 sheets defined 49.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 removed outlier: 4.752A pdb=" N GLU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.792A 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: 3.716A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 209 removed outlier: 4.239A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 239 removed outlier: 3.861A pdb=" N GLU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.685A pdb=" N VAL A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.879A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 314' Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.570A pdb=" N ALA A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 4.141A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.515A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.665A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 560 through 563 removed outlier: 3.572A 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: 3.507A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.762A pdb=" N ILE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 3.819A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.626A pdb=" N ILE A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 715 removed outlier: 4.098A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 762 removed outlier: 4.089A pdb=" N ALA A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Proline residue: A 743 - end of helix removed outlier: 3.624A pdb=" N PHE A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.807A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 810 Processing helix chain 'A' and resid 818 through 824 removed outlier: 4.266A pdb=" N ILE A 824 " --> pdb=" O PRO A 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.820A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.806A 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 177 through 181 removed outlier: 3.825A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.600A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.651A pdb=" N VAL B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.554A pdb=" N ALA B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 4.057A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.560A pdb=" N ALA B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.620A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 removed outlier: 3.945A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.549A 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: 3.903A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 636 removed outlier: 3.580A pdb=" N ILE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 3.611A pdb=" N CYS B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 654 " --> pdb=" O GLY B 650 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.360A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 715 removed outlier: 3.849A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 762 removed outlier: 3.665A pdb=" N ALA B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix removed outlier: 3.658A pdb=" N PHE B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.884A 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 788 removed outlier: 3.815A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.506A pdb=" N GLY B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 810 Processing helix chain 'B' and resid 812 through 818 Processing helix chain 'B' and resid 818 through 825 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.083A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.083A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN A 169 " --> pdb=" O MET A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 248 removed outlier: 7.843A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA6, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.515A pdb=" N GLU A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 523 removed outlier: 3.511A pdb=" N ILE A 523 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.304A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 248 removed outlier: 7.738A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB5, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB6, first strand: chain 'B' and resid 469 through 475 removed outlier: 3.656A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 480 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 523 through 524 removed outlier: 3.510A pdb=" N ILE B 523 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB9, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AC1, first strand: chain 'B' and resid 720 through 722 510 hydrogen bonds defined for protein. 1488 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: 4.61 Time building geometry restraints manager: 3.93 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: 2254 1.33 - 1.45: 3719 1.45 - 1.58: 6221 1.58 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 12358 Sorted by residual: bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.537 1.503 0.034 1.45e-02 4.76e+03 5.54e+00 bond pdb=" C GLU A 715 " pdb=" O GLU A 715 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.47e+00 bond pdb=" CA SER A 176 " pdb=" CB SER A 176 " ideal model delta sigma weight residual 1.529 1.492 0.036 1.66e-02 3.63e+03 4.78e+00 bond pdb=" CA SER A 235 " pdb=" CB SER A 235 " ideal model delta sigma weight residual 1.532 1.498 0.034 1.62e-02 3.81e+03 4.31e+00 bond pdb=" CA SER B 152 " pdb=" CB SER B 152 " ideal model delta sigma weight residual 1.528 1.496 0.033 1.59e-02 3.96e+03 4.18e+00 ... (remaining 12353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 15852 1.97 - 3.94: 870 3.94 - 5.90: 18 5.90 - 7.87: 4 7.87 - 9.84: 2 Bond angle restraints: 16746 Sorted by residual: angle pdb=" N PHE B 277 " pdb=" CA PHE B 277 " pdb=" C PHE B 277 " ideal model delta sigma weight residual 113.20 107.47 5.73 1.36e+00 5.41e-01 1.78e+01 angle pdb=" N GLU A 77 " pdb=" CA GLU A 77 " pdb=" C GLU A 77 " ideal model delta sigma weight residual 114.31 109.40 4.91 1.29e+00 6.01e-01 1.45e+01 angle pdb=" N VAL A 812 " pdb=" CA VAL A 812 " pdb=" C VAL A 812 " ideal model delta sigma weight residual 112.12 109.36 2.76 8.40e-01 1.42e+00 1.08e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 122.61 -9.84 3.00e+00 1.11e-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 112.77 122.49 -9.72 3.00e+00 1.11e-01 1.05e+01 ... (remaining 16741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 6885 22.53 - 45.06: 483 45.06 - 67.60: 74 67.60 - 90.13: 12 90.13 - 112.66: 16 Dihedral angle restraints: 7470 sinusoidal: 3016 harmonic: 4454 Sorted by residual: dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual -86.00 -13.09 -72.91 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 165.69 -72.69 1 1.00e+01 1.00e-02 6.74e+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 93.00 23.42 69.58 1 1.00e+01 1.00e-02 6.25e+01 ... (remaining 7467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1210 0.061 - 0.122: 584 0.122 - 0.184: 86 0.184 - 0.245: 4 0.245 - 0.306: 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 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+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 2.08e+00 chirality pdb=" CA PRO B 580 " pdb=" N PRO B 580 " pdb=" C PRO B 580 " pdb=" CB PRO B 580 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1883 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 901 " 0.033 2.00e-02 2.50e+03 2.75e-02 9.48e+00 pdb=" C7 NAG B 901 " -0.010 2.00e-02 2.50e+03 pdb=" C8 NAG B 901 " 0.026 2.00e-02 2.50e+03 pdb=" N2 NAG B 901 " -0.043 2.00e-02 2.50e+03 pdb=" O7 NAG B 901 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 96 " 0.200 9.50e-02 1.11e+02 8.97e-02 5.02e+00 pdb=" NE ARG B 96 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 96 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 96 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 96 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " -0.162 9.50e-02 1.11e+02 7.29e-02 3.63e+00 pdb=" NE ARG A 208 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " -0.002 2.00e-02 2.50e+03 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 728 2.73 - 3.27: 12751 3.27 - 3.82: 19586 3.82 - 4.36: 23606 4.36 - 4.90: 39576 Nonbonded interactions: 96247 Sorted by model distance: nonbonded pdb=" OD1 ASP A 545 " pdb=" OG1 THR A 548 " model vdw 2.191 3.040 nonbonded pdb=" O LEU B 752 " pdb=" OG1 THR B 755 " model vdw 2.204 3.040 nonbonded pdb=" O GLY A 624 " pdb=" OG SER A 654 " model vdw 2.215 3.040 nonbonded pdb=" CG2 ILE A 774 " pdb=" SD MET A 817 " model vdw 2.224 3.820 nonbonded pdb=" O LEU A 752 " pdb=" OG1 THR A 755 " model vdw 2.238 3.040 ... (remaining 96242 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: 3.800 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: 2.600 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.043 12380 Z= 0.444 Angle : 0.997 9.841 16792 Z= 0.671 Chirality : 0.064 0.306 1886 Planarity : 0.007 0.090 2112 Dihedral : 16.102 112.659 4554 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.97 % Favored : 91.83 % Rotamer: Outliers : 1.29 % Allowed : 13.99 % Favored : 84.72 % 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: -1.21 (0.21), residues: 1518 helix: 0.31 (0.20), residues: 671 sheet: -1.61 (0.47), residues: 123 loop : -1.74 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 532 HIS 0.009 0.003 HIS A 412 PHE 0.021 0.004 PHE B 112 TYR 0.026 0.004 TYR A 172 ARG 0.017 0.002 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 2) link_NAG-ASN : angle 1.28601 ( 6) hydrogen bonds : bond 0.15479 ( 510) hydrogen bonds : angle 5.66787 ( 1488) SS BOND : bond 0.00920 ( 20) SS BOND : angle 1.54595 ( 40) covalent geometry : bond 0.00671 (12358) covalent geometry : angle 0.99488 (16746) *********************** 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 128 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.841 Fit side-chains revert: symmetry clash REVERT: A 524 ARG cc_start: 0.8332 (mpp80) cc_final: 0.7347 (ptm160) REVERT: A 626 CYS cc_start: 0.9402 (t) cc_final: 0.9199 (m) REVERT: A 633 PHE cc_start: 0.8466 (m-80) cc_final: 0.7600 (m-80) REVERT: B 596 PHE cc_start: 0.7973 (t80) cc_final: 0.7632 (t80) outliers start: 17 outliers final: 5 residues processed: 123 average time/residue: 0.2516 time to fit residues: 47.6384 Evaluate side-chains 103 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 528 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 393 GLN ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 108 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.100512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063421 restraints weight = 30549.540| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.29 r_work: 0.2902 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12380 Z= 0.236 Angle : 0.664 7.502 16792 Z= 0.335 Chirality : 0.045 0.177 1886 Planarity : 0.004 0.041 2112 Dihedral : 9.253 75.930 1731 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.19 % Allowed : 15.96 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.90 (0.21), residues: 1518 helix: 0.80 (0.20), residues: 673 sheet: -1.49 (0.43), residues: 143 loop : -1.83 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 532 HIS 0.005 0.001 HIS A 267 PHE 0.016 0.001 PHE B 277 TYR 0.015 0.001 TYR A 645 ARG 0.011 0.001 ARG B 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 2) link_NAG-ASN : angle 0.77063 ( 6) hydrogen bonds : bond 0.04636 ( 510) hydrogen bonds : angle 4.43807 ( 1488) SS BOND : bond 0.00492 ( 20) SS BOND : angle 1.60531 ( 40) covalent geometry : bond 0.00550 (12358) covalent geometry : angle 0.65992 (16746) *********************** 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 135 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 633 PHE cc_start: 0.8119 (m-80) cc_final: 0.7185 (m-80) REVERT: A 817 MET cc_start: 0.8386 (tmm) cc_final: 0.7746 (tmm) REVERT: B 698 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.5233 (t80) REVERT: B 720 MET cc_start: 0.7895 (pmm) cc_final: 0.6896 (pmm) REVERT: B 779 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6423 (m-80) outliers start: 29 outliers final: 15 residues processed: 127 average time/residue: 0.2049 time to fit residues: 40.2095 Evaluate side-chains 120 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 3 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN B 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.101392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065949 restraints weight = 30621.548| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.05 r_work: 0.2889 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12380 Z= 0.148 Angle : 0.599 7.663 16792 Z= 0.297 Chirality : 0.043 0.199 1886 Planarity : 0.003 0.046 2112 Dihedral : 6.705 59.958 1726 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.42 % Allowed : 16.72 % Favored : 80.86 % 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: -0.74 (0.22), residues: 1518 helix: 0.93 (0.21), residues: 676 sheet: -1.50 (0.41), residues: 153 loop : -1.72 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 532 HIS 0.002 0.001 HIS B 218 PHE 0.022 0.001 PHE B 601 TYR 0.014 0.001 TYR A 645 ARG 0.002 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 2) link_NAG-ASN : angle 0.53720 ( 6) hydrogen bonds : bond 0.04042 ( 510) hydrogen bonds : angle 4.21494 ( 1488) SS BOND : bond 0.00411 ( 20) SS BOND : angle 1.22268 ( 40) covalent geometry : bond 0.00340 (12358) covalent geometry : angle 0.59712 (16746) *********************** 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 137 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 521 LYS cc_start: 0.7401 (pttp) cc_final: 0.6898 (ptpt) REVERT: A 633 PHE cc_start: 0.8272 (m-80) cc_final: 0.7351 (m-80) REVERT: A 817 MET cc_start: 0.8289 (tmm) cc_final: 0.7830 (tmm) REVERT: B 698 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.5534 (t80) REVERT: B 720 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7098 (pmm) REVERT: B 779 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6486 (m-80) outliers start: 32 outliers final: 20 residues processed: 125 average time/residue: 0.2133 time to fit residues: 41.0382 Evaluate side-chains 124 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 GLN ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.102237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066841 restraints weight = 30430.521| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.04 r_work: 0.2911 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12380 Z= 0.119 Angle : 0.590 10.902 16792 Z= 0.289 Chirality : 0.042 0.265 1886 Planarity : 0.003 0.048 2112 Dihedral : 5.390 58.716 1725 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.72 % Allowed : 17.40 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1518 helix: 1.04 (0.21), residues: 677 sheet: -1.41 (0.43), residues: 143 loop : -1.63 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.002 0.000 HIS B 74 PHE 0.015 0.001 PHE B 277 TYR 0.015 0.001 TYR A 645 ARG 0.002 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 2) link_NAG-ASN : angle 0.97908 ( 6) hydrogen bonds : bond 0.03639 ( 510) hydrogen bonds : angle 4.11071 ( 1488) SS BOND : bond 0.00354 ( 20) SS BOND : angle 1.70905 ( 40) covalent geometry : bond 0.00271 (12358) covalent geometry : angle 0.58502 (16746) *********************** 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 141 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7746 (mm) cc_final: 0.7310 (pp) REVERT: A 626 CYS cc_start: 0.9261 (t) cc_final: 0.8948 (m) REVERT: A 633 PHE cc_start: 0.8376 (m-80) cc_final: 0.7381 (m-80) REVERT: A 749 LEU cc_start: 0.9351 (mt) cc_final: 0.9150 (pp) REVERT: A 817 MET cc_start: 0.8351 (tmm) cc_final: 0.7865 (tmm) REVERT: B 720 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7106 (pmm) REVERT: B 779 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6477 (m-80) outliers start: 36 outliers final: 22 residues processed: 131 average time/residue: 0.2044 time to fit residues: 41.7738 Evaluate side-chains 129 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.101585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066195 restraints weight = 30365.081| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.28 r_work: 0.2879 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12380 Z= 0.147 Angle : 0.583 9.452 16792 Z= 0.287 Chirality : 0.042 0.250 1886 Planarity : 0.003 0.053 2112 Dihedral : 5.203 59.991 1724 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.56 % Allowed : 17.02 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.54 (0.22), residues: 1518 helix: 1.08 (0.21), residues: 679 sheet: -1.42 (0.43), residues: 143 loop : -1.60 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 532 HIS 0.003 0.001 HIS A 267 PHE 0.024 0.001 PHE B 601 TYR 0.015 0.001 TYR A 645 ARG 0.002 0.000 ARG B 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 2) link_NAG-ASN : angle 1.15157 ( 6) hydrogen bonds : bond 0.03725 ( 510) hydrogen bonds : angle 4.06701 ( 1488) SS BOND : bond 0.00390 ( 20) SS BOND : angle 1.36123 ( 40) covalent geometry : bond 0.00344 (12358) covalent geometry : angle 0.57942 (16746) *********************** 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 152 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 1.779 Fit side-chains REVERT: A 268 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7398 (pp) REVERT: A 626 CYS cc_start: 0.9301 (t) cc_final: 0.9009 (m) REVERT: A 633 PHE cc_start: 0.8407 (m-80) cc_final: 0.7406 (m-80) REVERT: A 786 LEU cc_start: 0.9499 (mp) cc_final: 0.9251 (pt) REVERT: A 817 MET cc_start: 0.8413 (tmm) cc_final: 0.7899 (tmm) REVERT: B 418 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8743 (mp) REVERT: B 720 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7089 (pmm) REVERT: B 756 PHE cc_start: 0.8686 (t80) cc_final: 0.8474 (t80) REVERT: B 779 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6555 (m-80) outliers start: 47 outliers final: 25 residues processed: 140 average time/residue: 0.2437 time to fit residues: 54.1892 Evaluate side-chains 129 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN ** B 641 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 = 0.3785 r_free = 0.3785 target = 0.098274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064005 restraints weight = 31124.150| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.97 r_work: 0.2795 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 12380 Z= 0.400 Angle : 0.768 12.804 16792 Z= 0.387 Chirality : 0.050 0.326 1886 Planarity : 0.004 0.051 2112 Dihedral : 5.872 65.324 1724 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.01 % Allowed : 17.02 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.21), residues: 1518 helix: 0.84 (0.21), residues: 678 sheet: -1.63 (0.40), residues: 151 loop : -1.87 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 532 HIS 0.006 0.002 HIS A 267 PHE 0.016 0.002 PHE A 277 TYR 0.016 0.002 TYR B 341 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 2) link_NAG-ASN : angle 2.30660 ( 6) hydrogen bonds : bond 0.04842 ( 510) hydrogen bonds : angle 4.41282 ( 1488) SS BOND : bond 0.00654 ( 20) SS BOND : angle 1.85750 ( 40) covalent geometry : bond 0.00943 (12358) covalent geometry : angle 0.76228 (16746) *********************** 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 159 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: A 626 CYS cc_start: 0.9343 (t) cc_final: 0.8990 (m) REVERT: A 633 PHE cc_start: 0.8191 (m-80) cc_final: 0.7048 (m-80) REVERT: A 779 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6980 (m-10) REVERT: A 802 MET cc_start: 0.8463 (mmp) cc_final: 0.7949 (mmm) REVERT: A 817 MET cc_start: 0.8626 (tmm) cc_final: 0.8061 (tmm) REVERT: B 202 MET cc_start: 0.9016 (mtp) cc_final: 0.8754 (mtp) REVERT: B 720 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7146 (pmm) REVERT: B 756 PHE cc_start: 0.8727 (t80) cc_final: 0.8519 (t80) REVERT: B 779 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6548 (m-80) outliers start: 53 outliers final: 31 residues processed: 145 average time/residue: 0.2401 time to fit residues: 53.9853 Evaluate side-chains 136 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.101142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.065409 restraints weight = 30478.397| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.17 r_work: 0.2864 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12380 Z= 0.134 Angle : 0.631 11.380 16792 Z= 0.306 Chirality : 0.043 0.257 1886 Planarity : 0.003 0.053 2112 Dihedral : 5.397 62.113 1724 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.03 % Allowed : 18.68 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1518 helix: 0.95 (0.21), residues: 677 sheet: -1.41 (0.39), residues: 161 loop : -1.68 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 532 HIS 0.004 0.001 HIS B 30 PHE 0.024 0.001 PHE B 601 TYR 0.015 0.001 TYR A 645 ARG 0.003 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 2) link_NAG-ASN : angle 1.28747 ( 6) hydrogen bonds : bond 0.03790 ( 510) hydrogen bonds : angle 4.16212 ( 1488) SS BOND : bond 0.00433 ( 20) SS BOND : angle 1.67664 ( 40) covalent geometry : bond 0.00310 (12358) covalent geometry : angle 0.62655 (16746) *********************** 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 142 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.414 Fit side-chains REVERT: A 477 ASP cc_start: 0.8042 (t0) cc_final: 0.7779 (t0) REVERT: A 633 PHE cc_start: 0.8339 (m-80) cc_final: 0.7400 (m-80) REVERT: A 779 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: A 788 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: A 817 MET cc_start: 0.8548 (tmm) cc_final: 0.7957 (tmm) REVERT: B 720 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7310 (pmm) REVERT: B 756 PHE cc_start: 0.8700 (t80) cc_final: 0.8483 (t80) REVERT: B 779 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6537 (m-80) outliers start: 40 outliers final: 28 residues processed: 128 average time/residue: 0.2483 time to fit residues: 50.2034 Evaluate side-chains 132 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.100589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066482 restraints weight = 31195.548| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.06 r_work: 0.2864 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 12380 Z= 0.187 Angle : 0.656 11.345 16792 Z= 0.319 Chirality : 0.044 0.278 1886 Planarity : 0.004 0.053 2112 Dihedral : 5.450 63.780 1724 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.03 % Allowed : 19.06 % Favored : 77.91 % 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: -0.67 (0.22), residues: 1518 helix: 0.98 (0.21), residues: 677 sheet: -1.44 (0.39), residues: 161 loop : -1.67 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 532 HIS 0.003 0.001 HIS B 30 PHE 0.015 0.001 PHE B 586 TYR 0.017 0.001 TYR A 746 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 1.55794 ( 6) hydrogen bonds : bond 0.03878 ( 510) hydrogen bonds : angle 4.19214 ( 1488) SS BOND : bond 0.00524 ( 20) SS BOND : angle 2.42503 ( 40) covalent geometry : bond 0.00448 (12358) covalent geometry : angle 0.64522 (16746) *********************** 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 142 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.558 Fit side-chains REVERT: A 477 ASP cc_start: 0.8376 (t0) cc_final: 0.8100 (t0) REVERT: A 626 CYS cc_start: 0.9391 (t) cc_final: 0.9004 (m) REVERT: A 633 PHE cc_start: 0.8413 (m-80) cc_final: 0.7494 (m-80) REVERT: A 779 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: A 817 MET cc_start: 0.8578 (tmm) cc_final: 0.7964 (tmm) REVERT: B 720 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7249 (pmm) REVERT: B 756 PHE cc_start: 0.8684 (t80) cc_final: 0.8464 (t80) REVERT: B 779 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6517 (m-80) outliers start: 40 outliers final: 29 residues processed: 130 average time/residue: 0.2890 time to fit residues: 60.2372 Evaluate side-chains 132 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 52 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066927 restraints weight = 30768.630| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.23 r_work: 0.2869 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 12380 Z= 0.145 Angle : 0.662 13.804 16792 Z= 0.321 Chirality : 0.042 0.184 1886 Planarity : 0.004 0.059 2112 Dihedral : 5.326 62.157 1724 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.50 % Allowed : 19.44 % Favored : 78.06 % 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: -0.67 (0.22), residues: 1518 helix: 0.97 (0.21), residues: 676 sheet: -1.66 (0.40), residues: 151 loop : -1.61 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.003 0.001 HIS B 30 PHE 0.029 0.001 PHE B 601 TYR 0.020 0.001 TYR A 645 ARG 0.002 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 2) link_NAG-ASN : angle 1.28375 ( 6) hydrogen bonds : bond 0.03588 ( 510) hydrogen bonds : angle 4.12927 ( 1488) SS BOND : bond 0.00413 ( 20) SS BOND : angle 3.08432 ( 40) covalent geometry : bond 0.00351 (12358) covalent geometry : angle 0.64506 (16746) *********************** 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 133 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.539 Fit side-chains REVERT: A 477 ASP cc_start: 0.8125 (t0) cc_final: 0.7865 (t0) REVERT: A 626 CYS cc_start: 0.9366 (t) cc_final: 0.8970 (m) REVERT: A 629 TYR cc_start: 0.8451 (m-80) cc_final: 0.8113 (m-10) REVERT: A 633 PHE cc_start: 0.8433 (m-80) cc_final: 0.7459 (m-80) REVERT: A 779 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: A 788 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: A 817 MET cc_start: 0.8573 (tmm) cc_final: 0.7935 (tmm) REVERT: B 418 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8758 (mp) REVERT: B 720 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7209 (pmm) REVERT: B 756 PHE cc_start: 0.8666 (t80) cc_final: 0.8450 (t80) REVERT: B 779 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6519 (m-80) outliers start: 33 outliers final: 25 residues processed: 122 average time/residue: 0.2841 time to fit residues: 54.5482 Evaluate side-chains 128 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065835 restraints weight = 30904.537| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.11 r_work: 0.2843 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 12380 Z= 0.255 Angle : 0.708 12.413 16792 Z= 0.347 Chirality : 0.045 0.314 1886 Planarity : 0.004 0.059 2112 Dihedral : 5.546 63.971 1724 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.65 % Allowed : 19.29 % Favored : 78.06 % 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: 0.94 (0.21), residues: 677 sheet: -1.64 (0.40), residues: 149 loop : -1.68 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 532 HIS 0.005 0.001 HIS A 267 PHE 0.016 0.001 PHE B 586 TYR 0.017 0.001 TYR A 645 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 2) link_NAG-ASN : angle 1.76149 ( 6) hydrogen bonds : bond 0.04014 ( 510) hydrogen bonds : angle 4.23219 ( 1488) SS BOND : bond 0.00610 ( 20) SS BOND : angle 3.03360 ( 40) covalent geometry : bond 0.00612 (12358) covalent geometry : angle 0.69212 (16746) ********************** 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 138 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.418 Fit side-chains REVERT: A 477 ASP cc_start: 0.8191 (t0) cc_final: 0.7921 (t0) REVERT: A 626 CYS cc_start: 0.9371 (t) cc_final: 0.8973 (m) REVERT: A 633 PHE cc_start: 0.8310 (m-80) cc_final: 0.7312 (m-80) REVERT: A 779 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6926 (m-10) REVERT: A 788 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: A 817 MET cc_start: 0.8558 (tmm) cc_final: 0.7985 (tmm) REVERT: B 720 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7231 (pmm) REVERT: B 756 PHE cc_start: 0.8680 (t80) cc_final: 0.8471 (t80) REVERT: B 779 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6554 (m-80) outliers start: 35 outliers final: 27 residues processed: 128 average time/residue: 0.2172 time to fit residues: 43.6345 Evaluate side-chains 131 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 788 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 779 TYR Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.101785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066959 restraints weight = 30739.954| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.35 r_work: 0.2867 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12380 Z= 0.132 Angle : 0.648 12.152 16792 Z= 0.313 Chirality : 0.042 0.191 1886 Planarity : 0.004 0.059 2112 Dihedral : 5.269 62.131 1724 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.42 % Allowed : 19.36 % Favored : 78.21 % 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: -0.65 (0.22), residues: 1518 helix: 0.99 (0.21), residues: 676 sheet: -1.67 (0.40), residues: 151 loop : -1.60 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.003 0.001 HIS B 30 PHE 0.019 0.001 PHE B 586 TYR 0.023 0.001 TYR A 746 ARG 0.002 0.000 ARG A 524 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 2) link_NAG-ASN : angle 1.13376 ( 6) hydrogen bonds : bond 0.03505 ( 510) hydrogen bonds : angle 4.09209 ( 1488) SS BOND : bond 0.00422 ( 20) SS BOND : angle 2.52004 ( 40) covalent geometry : bond 0.00317 (12358) covalent geometry : angle 0.63648 (16746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7963.81 seconds wall clock time: 143 minutes 9.07 seconds (8589.07 seconds total)