Starting phenix.real_space_refine on Sat Oct 11 05:59:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0e_37976/10_2025/8x0e_37976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0e_37976/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x0e_37976/10_2025/8x0e_37976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0e_37976/10_2025/8x0e_37976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0e_37976/10_2025/8x0e_37976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0e_37976/10_2025/8x0e_37976.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.65, per 1000 atoms: 0.22 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: 1.25 Conformation dependent library (CDL) restraints added in 616.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 2.02 Time building geometry restraints manager: 1.62 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: 0.02 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- 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 : 9.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.002 ARG A 292 TYR 0.026 0.004 TYR A 172 PHE 0.021 0.004 PHE B 112 TRP 0.023 0.004 TRP A 532 HIS 0.009 0.003 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00671 (12358) covalent geometry : angle 0.99488 (16746) SS BOND : bond 0.00920 ( 20) SS BOND : angle 1.54595 ( 40) hydrogen bonds : bond 0.15479 ( 510) hydrogen bonds : angle 5.66787 ( 1488) link_NAG-ASN : bond 0.00193 ( 2) link_NAG-ASN : angle 1.28601 ( 6) *********************** 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 : 0.322 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: 0.0909 time to fit residues: 17.2074 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 : 0.418 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 B 74 HIS B 108 GLN B 393 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.102607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068294 restraints weight = 30489.615| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.03 r_work: 0.2915 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12380 Z= 0.131 Angle : 0.615 7.516 16792 Z= 0.308 Chirality : 0.043 0.193 1886 Planarity : 0.003 0.042 2112 Dihedral : 9.035 74.650 1731 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.66 % Allowed : 16.04 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.22), residues: 1518 helix: 0.91 (0.21), residues: 667 sheet: -1.46 (0.42), residues: 153 loop : -1.70 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 524 TYR 0.016 0.001 TYR A 645 PHE 0.015 0.001 PHE A 818 TRP 0.011 0.001 TRP A 532 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00290 (12358) covalent geometry : angle 0.61247 (16746) SS BOND : bond 0.00353 ( 20) SS BOND : angle 1.25623 ( 40) hydrogen bonds : bond 0.04316 ( 510) hydrogen bonds : angle 4.32550 ( 1488) link_NAG-ASN : bond 0.00486 ( 2) link_NAG-ASN : angle 0.51874 ( 6) *********************** 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 127 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 521 LYS cc_start: 0.7264 (pttp) cc_final: 0.6833 (ptpt) REVERT: A 633 PHE cc_start: 0.8228 (m-80) cc_final: 0.7228 (m-80) REVERT: A 720 MET cc_start: 0.8767 (tmm) cc_final: 0.8553 (tmm) REVERT: A 817 MET cc_start: 0.8330 (tmm) cc_final: 0.7799 (tmm) REVERT: B 77 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: B 698 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.5223 (t80) REVERT: B 720 MET cc_start: 0.7858 (pmm) cc_final: 0.6819 (pmm) REVERT: B 779 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6474 (m-80) outliers start: 22 outliers final: 10 residues processed: 122 average time/residue: 0.0849 time to fit residues: 16.2160 Evaluate side-chains 115 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 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 77 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 528 VAL 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 25 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.101869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067064 restraints weight = 30835.455| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.37 r_work: 0.2876 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1400 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= 0.143 Angle : 0.592 7.346 16792 Z= 0.293 Chirality : 0.043 0.220 1886 Planarity : 0.003 0.046 2112 Dihedral : 6.298 57.816 1726 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.04 % Allowed : 16.87 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1518 helix: 0.99 (0.21), residues: 679 sheet: -1.42 (0.42), residues: 153 loop : -1.64 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.014 0.001 TYR A 645 PHE 0.022 0.001 PHE B 601 TRP 0.012 0.001 TRP A 532 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00331 (12358) covalent geometry : angle 0.58878 (16746) SS BOND : bond 0.00613 ( 20) SS BOND : angle 1.36790 ( 40) hydrogen bonds : bond 0.03973 ( 510) hydrogen bonds : angle 4.15324 ( 1488) link_NAG-ASN : bond 0.00505 ( 2) link_NAG-ASN : angle 0.51416 ( 6) *********************** 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 129 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7479 (pp) REVERT: A 633 PHE cc_start: 0.8271 (m-80) cc_final: 0.7260 (m-80) REVERT: A 817 MET cc_start: 0.8311 (tmm) cc_final: 0.7885 (tmm) REVERT: B 77 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: B 698 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5502 (t80) REVERT: B 720 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7042 (pmm) REVERT: B 756 PHE cc_start: 0.8633 (t80) cc_final: 0.8416 (t80) REVERT: B 779 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6503 (m-80) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 0.0807 time to fit residues: 15.2041 Evaluate side-chains 122 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS 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 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 77 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS 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 63 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** B 393 GLN B 470 ASN ** B 704 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 = 0.3811 r_free = 0.3811 target = 0.099591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065448 restraints weight = 30880.442| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.00 r_work: 0.2839 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12380 Z= 0.270 Angle : 0.666 8.252 16792 Z= 0.335 Chirality : 0.046 0.300 1886 Planarity : 0.004 0.047 2112 Dihedral : 5.697 63.913 1724 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.63 % Allowed : 16.72 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1518 helix: 0.95 (0.21), residues: 678 sheet: -1.34 (0.41), residues: 153 loop : -1.75 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.014 0.001 TYR A 746 PHE 0.017 0.001 PHE B 277 TRP 0.014 0.001 TRP A 532 HIS 0.005 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00638 (12358) covalent geometry : angle 0.65912 (16746) SS BOND : bond 0.00751 ( 20) SS BOND : angle 1.96158 ( 40) hydrogen bonds : bond 0.04380 ( 510) hydrogen bonds : angle 4.28646 ( 1488) link_NAG-ASN : bond 0.00359 ( 2) link_NAG-ASN : angle 1.55926 ( 6) *********************** 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 153 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 0.365 Fit side-chains REVERT: A 633 PHE cc_start: 0.8214 (m-80) cc_final: 0.7264 (m-80) REVERT: A 817 MET cc_start: 0.8488 (tmm) cc_final: 0.7944 (tmm) REVERT: B 77 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: B 416 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: B 698 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.5454 (t80) REVERT: B 720 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7015 (pmm) REVERT: B 756 PHE cc_start: 0.8688 (t80) cc_final: 0.8476 (t80) REVERT: B 779 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6510 (m-80) outliers start: 48 outliers final: 27 residues processed: 142 average time/residue: 0.0816 time to fit residues: 18.1362 Evaluate side-chains 133 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 77 GLU Chi-restraints excluded: chain B residue 85 LEU 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 416 MET Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 533 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** B 641 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 = 0.3825 r_free = 0.3825 target = 0.100345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065744 restraints weight = 30947.823| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.12 r_work: 0.2838 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1680 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= 0.202 Angle : 0.624 8.185 16792 Z= 0.310 Chirality : 0.044 0.207 1886 Planarity : 0.003 0.049 2112 Dihedral : 5.499 62.209 1724 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.63 % Allowed : 17.62 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1518 helix: 0.99 (0.21), residues: 675 sheet: -1.36 (0.41), residues: 153 loop : -1.72 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.014 0.001 TYR A 645 PHE 0.024 0.001 PHE B 601 TRP 0.011 0.001 TRP A 532 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00476 (12358) covalent geometry : angle 0.62036 (16746) SS BOND : bond 0.00416 ( 20) SS BOND : angle 1.44423 ( 40) hydrogen bonds : bond 0.04039 ( 510) hydrogen bonds : angle 4.18164 ( 1488) link_NAG-ASN : bond 0.00401 ( 2) link_NAG-ASN : angle 1.41074 ( 6) *********************** 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 149 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 633 PHE cc_start: 0.8319 (m-80) cc_final: 0.7384 (m-80) REVERT: A 817 MET cc_start: 0.8470 (tmm) cc_final: 0.7953 (tmm) REVERT: B 418 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B 698 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.5510 (t80) REVERT: B 720 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7146 (pmm) REVERT: B 779 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6543 (m-80) outliers start: 48 outliers final: 28 residues processed: 138 average time/residue: 0.0830 time to fit residues: 17.7514 Evaluate side-chains 133 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 214 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 492 LEU Chi-restraints excluded: chain A residue 499 VAL 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 776 PHE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 85 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.101510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065795 restraints weight = 30803.081| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.18 r_work: 0.2878 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12380 Z= 0.131 Angle : 0.591 9.137 16792 Z= 0.291 Chirality : 0.042 0.177 1886 Planarity : 0.003 0.052 2112 Dihedral : 5.227 60.815 1724 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.25 % Allowed : 17.70 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.22), residues: 1518 helix: 1.04 (0.21), residues: 678 sheet: -1.67 (0.38), residues: 172 loop : -1.65 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 524 TYR 0.017 0.001 TYR A 746 PHE 0.013 0.001 PHE B 586 TRP 0.010 0.001 TRP A 532 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00303 (12358) covalent geometry : angle 0.58789 (16746) SS BOND : bond 0.00480 ( 20) SS BOND : angle 1.37643 ( 40) hydrogen bonds : bond 0.03663 ( 510) hydrogen bonds : angle 4.06646 ( 1488) link_NAG-ASN : bond 0.00381 ( 2) link_NAG-ASN : angle 1.08733 ( 6) *********************** 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 146 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 477 ASP cc_start: 0.7971 (t0) cc_final: 0.7762 (t0) REVERT: A 626 CYS cc_start: 0.9285 (t) cc_final: 0.8922 (m) REVERT: A 633 PHE cc_start: 0.8402 (m-80) cc_final: 0.7376 (m-80) REVERT: A 738 LEU cc_start: 0.7886 (pt) cc_final: 0.7560 (mp) REVERT: A 779 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: A 802 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: A 817 MET cc_start: 0.8464 (tmm) cc_final: 0.7937 (tmm) REVERT: B 277 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: B 418 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 720 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7118 (pmm) REVERT: B 779 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6591 (m-80) outliers start: 43 outliers final: 25 residues processed: 135 average time/residue: 0.0757 time to fit residues: 16.1461 Evaluate side-chains 133 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 214 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 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 802 MET 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 277 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 0.0870 chunk 63 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.102238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066965 restraints weight = 30762.207| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.02 r_work: 0.2906 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1923 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= 0.111 Angle : 0.589 10.403 16792 Z= 0.284 Chirality : 0.041 0.215 1886 Planarity : 0.003 0.053 2112 Dihedral : 5.023 59.991 1724 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.72 % Allowed : 18.76 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1518 helix: 1.09 (0.21), residues: 678 sheet: -1.51 (0.40), residues: 167 loop : -1.53 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 524 TYR 0.019 0.001 TYR A 746 PHE 0.028 0.001 PHE B 601 TRP 0.010 0.001 TRP A 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00250 (12358) covalent geometry : angle 0.58601 (16746) SS BOND : bond 0.00332 ( 20) SS BOND : angle 1.26696 ( 40) hydrogen bonds : bond 0.03462 ( 510) hydrogen bonds : angle 4.04638 ( 1488) link_NAG-ASN : bond 0.00389 ( 2) link_NAG-ASN : angle 0.88198 ( 6) *********************** 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 141 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.471 Fit side-chains REVERT: A 268 LEU cc_start: 0.7792 (mm) cc_final: 0.7413 (pp) REVERT: A 477 ASP cc_start: 0.7971 (t0) cc_final: 0.7764 (t0) REVERT: A 626 CYS cc_start: 0.9400 (t) cc_final: 0.8990 (m) REVERT: A 629 TYR cc_start: 0.8436 (m-80) cc_final: 0.8115 (m-10) REVERT: A 633 PHE cc_start: 0.8459 (m-80) cc_final: 0.7516 (m-80) REVERT: A 738 LEU cc_start: 0.7885 (pt) cc_final: 0.7565 (mp) REVERT: A 779 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6981 (m-10) REVERT: A 788 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: A 802 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7621 (mmm) REVERT: A 817 MET cc_start: 0.8375 (tmm) cc_final: 0.7858 (tmm) REVERT: B 277 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: B 418 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8681 (mp) REVERT: B 720 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7176 (pmm) REVERT: B 756 PHE cc_start: 0.8685 (t80) cc_final: 0.8463 (t80) REVERT: B 779 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6612 (m-80) outliers start: 36 outliers final: 23 residues processed: 129 average time/residue: 0.0913 time to fit residues: 18.6218 Evaluate side-chains 129 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 596 PHE 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 802 MET 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 112 PHE Chi-restraints excluded: chain B residue 267 HIS 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 418 LEU Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 444 THR 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 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 82 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.101270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065938 restraints weight = 30586.641| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.05 r_work: 0.2874 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12380 Z= 0.168 Angle : 0.611 9.930 16792 Z= 0.297 Chirality : 0.043 0.297 1886 Planarity : 0.003 0.053 2112 Dihedral : 5.086 61.244 1724 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.10 % Allowed : 18.46 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1518 helix: 1.09 (0.21), residues: 678 sheet: -1.58 (0.39), residues: 167 loop : -1.55 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.020 0.001 TYR A 746 PHE 0.016 0.001 PHE B 586 TRP 0.010 0.001 TRP A 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00397 (12358) covalent geometry : angle 0.60759 (16746) SS BOND : bond 0.00381 ( 20) SS BOND : angle 1.39181 ( 40) hydrogen bonds : bond 0.03685 ( 510) hydrogen bonds : angle 4.05160 ( 1488) link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 1.13281 ( 6) *********************** 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 140 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.472 Fit side-chains REVERT: A 268 LEU cc_start: 0.7846 (mm) cc_final: 0.7373 (pp) REVERT: A 477 ASP cc_start: 0.7982 (t0) cc_final: 0.7777 (t0) REVERT: A 626 CYS cc_start: 0.9368 (t) cc_final: 0.8967 (m) REVERT: A 633 PHE cc_start: 0.8429 (m-80) cc_final: 0.7501 (m-80) REVERT: A 738 LEU cc_start: 0.7901 (pt) cc_final: 0.7574 (mp) REVERT: A 779 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: A 788 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: A 802 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7660 (mmm) REVERT: A 817 MET cc_start: 0.8505 (tmm) cc_final: 0.8014 (tmm) REVERT: B 277 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: B 720 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7201 (pmm) REVERT: B 756 PHE cc_start: 0.8687 (t80) cc_final: 0.8474 (t80) REVERT: B 779 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6598 (m-80) outliers start: 41 outliers final: 29 residues processed: 128 average time/residue: 0.0822 time to fit residues: 16.8635 Evaluate side-chains 133 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 406 SER 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 788 PHE Chi-restraints excluded: chain A residue 802 MET 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 277 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 444 THR 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 130 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.100997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066671 restraints weight = 30653.160| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.21 r_work: 0.2863 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 12380 Z= 0.190 Angle : 0.649 13.245 16792 Z= 0.317 Chirality : 0.044 0.292 1886 Planarity : 0.003 0.058 2112 Dihedral : 5.225 61.728 1724 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.40 % Allowed : 18.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1518 helix: 1.03 (0.21), residues: 678 sheet: -1.39 (0.41), residues: 151 loop : -1.56 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.022 0.001 TYR A 746 PHE 0.029 0.001 PHE B 601 TRP 0.011 0.001 TRP A 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00454 (12358) covalent geometry : angle 0.63764 (16746) SS BOND : bond 0.00379 ( 20) SS BOND : angle 2.56160 ( 40) hydrogen bonds : bond 0.03761 ( 510) hydrogen bonds : angle 4.08384 ( 1488) link_NAG-ASN : bond 0.00258 ( 2) link_NAG-ASN : angle 1.26047 ( 6) *********************** 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 142 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.434 Fit side-chains REVERT: A 268 LEU cc_start: 0.7880 (mm) cc_final: 0.7302 (pp) REVERT: A 477 ASP cc_start: 0.8055 (t0) cc_final: 0.7846 (t0) REVERT: A 519 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7378 (pp30) REVERT: A 626 CYS cc_start: 0.9372 (t) cc_final: 0.8966 (m) REVERT: A 633 PHE cc_start: 0.8446 (m-80) cc_final: 0.7478 (m-80) REVERT: A 779 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: A 788 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: A 802 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: A 817 MET cc_start: 0.8512 (tmm) cc_final: 0.7811 (tmm) REVERT: B 720 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7222 (pmm) REVERT: B 756 PHE cc_start: 0.8718 (t80) cc_final: 0.8503 (t80) REVERT: B 779 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6576 (m-80) outliers start: 45 outliers final: 32 residues processed: 129 average time/residue: 0.0712 time to fit residues: 14.8191 Evaluate side-chains 134 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 277 PHE 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 492 LEU 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 519 GLN 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 802 MET 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 146 VAL 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 419 CYS Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 444 THR 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 67 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.100871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065692 restraints weight = 30770.586| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.41 r_work: 0.2835 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 12380 Z= 0.190 Angle : 0.651 12.724 16792 Z= 0.317 Chirality : 0.044 0.285 1886 Planarity : 0.004 0.057 2112 Dihedral : 5.249 62.035 1724 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % 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 : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1518 helix: 1.03 (0.20), residues: 678 sheet: -1.45 (0.40), residues: 151 loop : -1.56 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.022 0.001 TYR A 746 PHE 0.016 0.001 PHE B 586 TRP 0.011 0.001 TRP A 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00455 (12358) covalent geometry : angle 0.63984 (16746) SS BOND : bond 0.00464 ( 20) SS BOND : angle 2.48347 ( 40) hydrogen bonds : bond 0.03757 ( 510) hydrogen bonds : angle 4.07709 ( 1488) link_NAG-ASN : bond 0.00270 ( 2) link_NAG-ASN : angle 1.28360 ( 6) ********************** 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: 40 poor density : 98 time to evaluate : 0.353 Fit side-chains REVERT: A 268 LEU cc_start: 0.7852 (mm) cc_final: 0.7289 (pp) REVERT: A 477 ASP cc_start: 0.8094 (t0) cc_final: 0.7877 (t0) REVERT: A 519 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7110 (pp30) REVERT: A 626 CYS cc_start: 0.9375 (t) cc_final: 0.8971 (m) REVERT: A 633 PHE cc_start: 0.8458 (m-80) cc_final: 0.7475 (m-80) REVERT: A 779 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6965 (m-10) REVERT: A 788 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: A 802 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: A 817 MET cc_start: 0.8417 (tmm) cc_final: 0.7600 (tmm) REVERT: B 720 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7232 (pmm) REVERT: B 756 PHE cc_start: 0.8664 (t80) cc_final: 0.8447 (t80) REVERT: B 779 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6572 (m-80) outliers start: 40 outliers final: 31 residues processed: 125 average time/residue: 0.0777 time to fit residues: 15.3575 Evaluate side-chains 132 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 492 LEU 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 519 GLN Chi-restraints excluded: chain A residue 521 LYS 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 802 MET 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 419 CYS Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 444 THR 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 68 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.101521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.066758 restraints weight = 30888.798| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.05 r_work: 0.2896 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 12380 Z= 0.148 Angle : 0.648 12.332 16792 Z= 0.315 Chirality : 0.043 0.272 1886 Planarity : 0.003 0.058 2112 Dihedral : 5.262 61.547 1724 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.10 % Allowed : 18.53 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.22), residues: 1518 helix: 1.05 (0.21), residues: 678 sheet: -1.51 (0.39), residues: 161 loop : -1.59 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 524 TYR 0.022 0.001 TYR A 746 PHE 0.028 0.001 PHE B 601 TRP 0.009 0.001 TRP A 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00359 (12358) covalent geometry : angle 0.63209 (16746) SS BOND : bond 0.00419 ( 20) SS BOND : angle 2.93705 ( 40) hydrogen bonds : bond 0.03584 ( 510) hydrogen bonds : angle 4.02635 ( 1488) link_NAG-ASN : bond 0.00268 ( 2) link_NAG-ASN : angle 1.18348 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.33 seconds wall clock time: 54 minutes 55.52 seconds (3295.52 seconds total)