Starting phenix.real_space_refine on Wed Aug 5 20:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6j_41069/08_2026/8t6j_41069.map" } resolution = 3.5 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= 0.000 sd= 1.000 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 112 5.16 5 C 7473 2.51 5 N 1940 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5803 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5793 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 156 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.18, per 1000 atoms: 0.27 Number of scatterers: 11652 At special positions: 0 Unit cell: (123.555, 82.6537, 188.314, 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 112 16.00 O 2127 8.00 N 1940 7.00 C 7473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 662.2 milliseconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 51.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.670A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.500A pdb=" N ALA B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.896A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.889A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.975A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.666A pdb=" N ARG B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.378A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.807A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.923A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 removed outlier: 3.929A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.833A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.694A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 630 Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.723A pdb=" N ALA B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 4.223A pdb=" N CYS B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.272A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 3.535A pdb=" N GLN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 4.097A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 793 removed outlier: 3.594A pdb=" N ASN B 769 " --> pdb=" O PRO B 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 797 through 816 removed outlier: 3.931A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.742A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.685A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.883A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.585A 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 177 through 181 removed outlier: 3.893A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.729A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.655A pdb=" N ARG A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.558A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 4.388A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.790A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.930A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.072A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.895A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.859A pdb=" N VAL A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.697A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.662A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 4.241A pdb=" N CYS A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 4.298A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 removed outlier: 3.523A pdb=" N GLN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 Proline residue: A 743 - end of helix removed outlier: 4.044A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 793 removed outlier: 3.582A pdb=" N ASN A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.262A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 213 through 216 removed outlier: 7.768A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.291A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 468 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'B' and resid 471 through 475 removed outlier: 3.570A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 480 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.609A pdb=" N ASP B 722 " --> pdb=" O TYR B 730 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.258A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216 removed outlier: 7.759A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 472 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 480 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 468 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB8, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AB9, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.606A pdb=" N ASP A 722 " --> pdb=" O TYR A 730 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1527 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: 1.87 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1887 1.27 - 1.41: 3001 1.41 - 1.55: 6857 1.55 - 1.68: 11 1.68 - 1.82: 162 Bond restraints: 11918 Sorted by residual: bond pdb=" C19 YKU B 901 " pdb=" C21 YKU B 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C19 YKU A 901 " pdb=" C21 YKU A 901 " ideal model delta sigma weight residual 1.429 1.526 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C13 YKU A 901 " pdb=" N12 YKU A 901 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 YKU B 901 " pdb=" N12 YKU B 901 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C04 YKU B 901 " pdb=" C07 YKU B 901 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.87e+00 ... (remaining 11913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 15964 2.00 - 4.00: 222 4.00 - 6.00: 19 6.00 - 7.99: 3 7.99 - 9.99: 2 Bond angle restraints: 16210 Sorted by residual: angle pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " pdb=" CD LYS B 51 " ideal model delta sigma weight residual 111.30 117.90 -6.60 2.30e+00 1.89e-01 8.23e+00 angle pdb=" CA LEU B 295 " pdb=" CB LEU B 295 " pdb=" CG LEU B 295 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.15e+00 angle pdb=" CB ARG B 114 " pdb=" CG ARG B 114 " pdb=" CD ARG B 114 " ideal model delta sigma weight residual 111.30 104.76 6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" CB MET A 474 " pdb=" CG MET A 474 " pdb=" SD MET A 474 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" CB LYS A 51 " pdb=" CG LYS A 51 " pdb=" CD LYS A 51 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.71e+00 ... (remaining 16205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6401 17.97 - 35.94: 567 35.94 - 53.91: 105 53.91 - 71.88: 20 71.88 - 89.85: 3 Dihedral angle restraints: 7096 sinusoidal: 2638 harmonic: 4458 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 135.61 -42.61 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -44.07 -41.93 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual 93.00 134.68 -41.68 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 7093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1000 0.027 - 0.054: 531 0.054 - 0.082: 203 0.082 - 0.109: 84 0.109 - 0.136: 34 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 568 " pdb=" N ILE B 568 " pdb=" C ILE B 568 " pdb=" CB ILE B 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 568 " pdb=" N ILE A 568 " pdb=" C ILE A 568 " pdb=" CB ILE A 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL B 217 " pdb=" N VAL B 217 " pdb=" C VAL B 217 " pdb=" CB VAL B 217 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1849 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 789 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 790 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 790 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 790 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 789 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 790 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 790 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 790 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 764 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 765 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 791 2.74 - 3.28: 11449 3.28 - 3.82: 18007 3.82 - 4.36: 19638 4.36 - 4.90: 36335 Nonbonded interactions: 86220 Sorted by model distance: nonbonded pdb=" OG SER B 152 " pdb=" OG SER B 176 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.221 3.040 nonbonded pdb=" O ARG B 435 " pdb=" NH1 ARG B 435 " model vdw 2.228 3.120 nonbonded pdb=" O ARG A 435 " pdb=" NH1 ARG A 435 " model vdw 2.229 3.120 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.274 3.040 ... (remaining 86215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 515 or (resid 516 through 517 and (name N or na \ me CA or name C or name O or name CB )) or resid 518 through 901)) selection = (chain 'B' and (resid 26 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 552 or (resid 553 and (name N o \ r name CA or name C or name O or name CB )) or resid 554 through 559 or (resid 5 \ 60 through 561 and (name N or name CA or name C or name O or name CB )) or resid \ 562 through 901)) } 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 group one per residue 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: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 12.010 Find NCS groups from input model: 0.220 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.003 0.098 11934 Z= 0.169 Angle : 0.564 9.992 16242 Z= 0.290 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.036 2058 Dihedral : 13.807 89.854 4184 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -0.00 (0.23), residues: 1522 helix: 1.52 (0.21), residues: 648 sheet: -1.22 (0.42), residues: 172 loop : -1.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 114 TYR 0.010 0.001 TYR B 223 PHE 0.013 0.001 PHE B 544 TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (11918) covalent geometry : angle 0.56267 / 0.29 (16210) SS BOND : bond 0.00179 / 0.12 ( 16) SS BOND : angle 1.03347 / 0.70 ( 32) hydrogen bonds : bond 0.14829 / 9.57 ( 527) hydrogen bonds : angle 5.56016 / 3.82 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 657 MET cc_start: 0.6699 (ptm) cc_final: 0.6420 (ptt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0835 time to fit residues: 19.7598 Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0030 chunk 130 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.4482 > 50:) chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 747 ASN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.141315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.116551 restraints weight = 22047.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116159 restraints weight = 16398.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117041 restraints weight = 16805.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117422 restraints weight = 12822.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117974 restraints weight = 12215.290| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11934 Z= 0.218 Angle : 0.617 6.676 16242 Z= 0.323 Chirality : 0.045 0.164 1852 Planarity : 0.004 0.049 2058 Dihedral : 4.969 36.419 1662 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.98 % Allowed : 9.00 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -0.10 (0.22), residues: 1522 helix: 1.46 (0.21), residues: 662 sheet: -1.41 (0.40), residues: 184 loop : -1.21 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 114 TYR 0.021 0.002 TYR B 340 PHE 0.020 0.002 PHE A 712 TRP 0.013 0.002 TRP A 487 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (11918) covalent geometry : angle 0.61506 / 0.32 (16210) SS BOND : bond 0.00312 / 0.22 ( 16) SS BOND : angle 1.15957 / 0.76 ( 32) hydrogen bonds : bond 0.05332 / 3.58 ( 527) hydrogen bonds : angle 4.38420 / 3.00 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6130 (mt-10) REVERT: A 416 MET cc_start: 0.8032 (ttp) cc_final: 0.7800 (ttp) outliers start: 24 outliers final: 14 residues processed: 146 average time/residue: 0.0813 time to fit residues: 17.9337 Evaluate side-chains 141 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 33 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118865 restraints weight = 22272.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118325 restraints weight = 16133.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119382 restraints weight = 14817.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119650 restraints weight = 12015.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120086 restraints weight = 11610.748| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11934 Z= 0.113 Angle : 0.504 5.859 16242 Z= 0.263 Chirality : 0.041 0.146 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.533 30.972 1662 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.90 % Allowed : 10.90 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.23 (0.23), residues: 1522 helix: 1.71 (0.21), residues: 658 sheet: -1.23 (0.41), residues: 172 loop : -1.02 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 524 TYR 0.018 0.001 TYR A 340 PHE 0.019 0.001 PHE A 712 TRP 0.008 0.001 TRP A 359 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (11918) covalent geometry : angle 0.50299 / 0.26 (16210) SS BOND : bond 0.00232 / 0.16 ( 16) SS BOND : angle 0.98221 / 0.63 ( 32) hydrogen bonds : bond 0.04060 / 2.75 ( 527) hydrogen bonds : angle 4.00095 / 2.74 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 601 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6553 (t80) REVERT: B 657 MET cc_start: 0.6936 (ptm) cc_final: 0.6611 (ptt) REVERT: A 416 MET cc_start: 0.7976 (ttp) cc_final: 0.7743 (ttp) REVERT: A 601 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6517 (t80) outliers start: 23 outliers final: 13 residues processed: 146 average time/residue: 0.0827 time to fit residues: 18.4616 Evaluate side-chains 140 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 89 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.144784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119796 restraints weight = 22102.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119131 restraints weight = 16483.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120198 restraints weight = 15346.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120422 restraints weight = 12414.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120885 restraints weight = 12134.885| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11934 Z= 0.103 Angle : 0.490 7.214 16242 Z= 0.253 Chirality : 0.041 0.145 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.288 26.915 1662 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.90 % Allowed : 12.30 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.29 (0.22), residues: 1522 helix: 1.79 (0.21), residues: 652 sheet: -1.21 (0.41), residues: 172 loop : -1.00 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 524 TYR 0.013 0.001 TYR A 629 PHE 0.025 0.001 PHE A 712 TRP 0.008 0.001 TRP A 359 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (11918) covalent geometry : angle 0.48884 / 0.25 (16210) SS BOND : bond 0.00208 / 0.14 ( 16) SS BOND : angle 0.82849 / 0.53 ( 32) hydrogen bonds : bond 0.03654 / 2.47 ( 527) hydrogen bonds : angle 3.78061 / 2.59 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 601 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6586 (t80) REVERT: B 688 MET cc_start: 0.6737 (mmt) cc_final: 0.6397 (mmt) REVERT: A 416 MET cc_start: 0.7953 (ttp) cc_final: 0.7713 (ttp) REVERT: A 601 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6547 (t80) outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 0.0895 time to fit residues: 20.7103 Evaluate side-chains 147 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119956 restraints weight = 22097.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118910 restraints weight = 16845.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119673 restraints weight = 18686.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120224 restraints weight = 13861.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120747 restraints weight = 12763.580| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11934 Z= 0.105 Angle : 0.494 8.786 16242 Z= 0.254 Chirality : 0.041 0.146 1852 Planarity : 0.003 0.038 2058 Dihedral : 4.157 24.287 1662 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.82 % Allowed : 12.63 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.32 (0.22), residues: 1522 helix: 1.79 (0.21), residues: 656 sheet: -1.17 (0.41), residues: 172 loop : -0.96 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 524 TYR 0.015 0.001 TYR A 629 PHE 0.025 0.001 PHE A 712 TRP 0.007 0.001 TRP A 359 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11918) covalent geometry : angle 0.49312 / 0.25 (16210) SS BOND : bond 0.00189 / 0.13 ( 16) SS BOND : angle 0.72655 / 0.47 ( 32) hydrogen bonds : bond 0.03562 / 2.41 ( 527) hydrogen bonds : angle 3.67478 / 2.52 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7157 (mtp85) REVERT: B 474 MET cc_start: 0.7945 (mmp) cc_final: 0.7717 (mmm) REVERT: B 601 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6581 (t80) REVERT: B 657 MET cc_start: 0.6933 (ptm) cc_final: 0.6480 (ptt) REVERT: B 688 MET cc_start: 0.6699 (mmt) cc_final: 0.6318 (mmt) REVERT: A 416 MET cc_start: 0.7956 (ttp) cc_final: 0.7716 (ttp) REVERT: A 601 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6559 (t80) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.0904 time to fit residues: 20.7212 Evaluate side-chains 146 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.142753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117580 restraints weight = 22107.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117001 restraints weight = 16563.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117963 restraints weight = 15534.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118205 restraints weight = 12714.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118589 restraints weight = 12524.757| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11934 Z= 0.154 Angle : 0.540 11.336 16242 Z= 0.276 Chirality : 0.042 0.149 1852 Planarity : 0.004 0.033 2058 Dihedral : 4.274 21.154 1662 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.23 % Allowed : 13.63 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.19 (0.22), residues: 1522 helix: 1.73 (0.21), residues: 658 sheet: -1.35 (0.39), residues: 184 loop : -1.05 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 524 TYR 0.017 0.001 TYR A 629 PHE 0.027 0.001 PHE A 712 TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (11918) covalent geometry : angle 0.53934 / 0.28 (16210) SS BOND : bond 0.00226 / 0.16 ( 16) SS BOND : angle 0.74484 / 0.47 ( 32) hydrogen bonds : bond 0.04273 / 2.87 ( 527) hydrogen bonds : angle 3.76873 / 2.58 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8034 (mmp) cc_final: 0.7787 (mmp) REVERT: B 601 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6595 (t80) REVERT: B 657 MET cc_start: 0.7010 (ptm) cc_final: 0.6806 (ptt) REVERT: B 688 MET cc_start: 0.6726 (mmt) cc_final: 0.6331 (mmt) REVERT: A 79 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7691 (tt) REVERT: A 474 MET cc_start: 0.7862 (mmp) cc_final: 0.7626 (mmm) REVERT: A 601 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6580 (t80) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.0848 time to fit residues: 19.6227 Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119013 restraints weight = 21963.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118261 restraints weight = 16302.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119161 restraints weight = 17432.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119632 restraints weight = 13098.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120098 restraints weight = 12222.927| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11934 Z= 0.107 Angle : 0.507 11.675 16242 Z= 0.257 Chirality : 0.041 0.149 1852 Planarity : 0.003 0.032 2058 Dihedral : 4.087 19.599 1662 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.15 % Allowed : 14.86 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.26 (0.22), residues: 1522 helix: 1.70 (0.20), residues: 670 sheet: -1.20 (0.41), residues: 172 loop : -1.01 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 524 TYR 0.018 0.001 TYR A 629 PHE 0.024 0.001 PHE A 712 TRP 0.007 0.001 TRP B 575 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11918) covalent geometry : angle 0.50608 / 0.26 (16210) SS BOND : bond 0.00198 / 0.14 ( 16) SS BOND : angle 0.73027 / 0.46 ( 32) hydrogen bonds : bond 0.03641 / 2.46 ( 527) hydrogen bonds : angle 3.63672 / 2.49 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8041 (mmp) cc_final: 0.7798 (mmp) REVERT: B 601 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6537 (t80) REVERT: B 688 MET cc_start: 0.6799 (mmt) cc_final: 0.6425 (mmt) REVERT: A 474 MET cc_start: 0.7980 (mmp) cc_final: 0.7765 (mmm) REVERT: A 601 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6468 (t80) outliers start: 26 outliers final: 21 residues processed: 149 average time/residue: 0.0752 time to fit residues: 17.2420 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.1980 chunk 123 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 0.0030 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 0.0670 chunk 119 optimal weight: 0.9980 overall best weight: 0.1126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121402 restraints weight = 22109.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120958 restraints weight = 15903.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121741 restraints weight = 17426.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122209 restraints weight = 13102.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122665 restraints weight = 12061.888| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11934 Z= 0.092 Angle : 0.499 12.878 16242 Z= 0.249 Chirality : 0.040 0.170 1852 Planarity : 0.003 0.033 2058 Dihedral : 3.860 18.280 1662 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 14.95 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.40 (0.22), residues: 1522 helix: 1.77 (0.20), residues: 678 sheet: -1.11 (0.41), residues: 172 loop : -0.91 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 524 TYR 0.016 0.001 TYR A 629 PHE 0.023 0.001 PHE A 712 TRP 0.008 0.001 TRP B 359 HIS 0.002 0.000 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (11918) covalent geometry : angle 0.49843 / 0.25 (16210) SS BOND : bond 0.00172 / 0.12 ( 16) SS BOND : angle 0.66610 / 0.42 ( 32) hydrogen bonds : bond 0.03028 / 2.06 ( 527) hydrogen bonds : angle 3.47429 / 2.38 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7129 (mtp85) REVERT: B 474 MET cc_start: 0.7946 (mmp) cc_final: 0.7719 (mmp) REVERT: B 601 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 688 MET cc_start: 0.6646 (mmt) cc_final: 0.6321 (mmt) REVERT: A 345 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7095 (mtp85) REVERT: A 601 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6580 (t80) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.0975 time to fit residues: 22.3286 Evaluate side-chains 144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.140221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114261 restraints weight = 21942.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114412 restraints weight = 16982.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115146 restraints weight = 15984.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115563 restraints weight = 12530.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116032 restraints weight = 11935.089| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11934 Z= 0.251 Angle : 0.657 14.892 16242 Z= 0.337 Chirality : 0.046 0.152 1852 Planarity : 0.005 0.052 2058 Dihedral : 4.568 21.338 1662 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 2.23 % Allowed : 15.28 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -0.03 (0.22), residues: 1522 helix: 1.51 (0.20), residues: 662 sheet: -1.48 (0.39), residues: 184 loop : -1.14 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 648 TYR 0.022 0.002 TYR B 629 PHE 0.025 0.002 PHE A 712 TRP 0.021 0.002 TRP A 575 HIS 0.008 0.002 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (11918) covalent geometry : angle 0.65624 / 0.34 (16210) SS BOND : bond 0.00286 / 0.20 ( 16) SS BOND : angle 0.88124 / 0.55 ( 32) hydrogen bonds : bond 0.05578 / 3.73 ( 527) hydrogen bonds : angle 3.97843 / 2.71 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8109 (mmp) cc_final: 0.7835 (mmp) REVERT: B 494 MET cc_start: 0.9402 (ttt) cc_final: 0.9184 (ttt) REVERT: B 601 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6627 (t80) REVERT: A 79 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7743 (tt) REVERT: A 497 ASP cc_start: 0.7247 (t0) cc_final: 0.7047 (t0) REVERT: A 601 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6620 (t80) outliers start: 27 outliers final: 21 residues processed: 143 average time/residue: 0.0862 time to fit residues: 19.2224 Evaluate side-chains 145 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.142973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118811 restraints weight = 21993.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117809 restraints weight = 19083.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118657 restraints weight = 19585.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118910 restraints weight = 15266.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119256 restraints weight = 14841.358| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11934 Z= 0.132 Angle : 0.557 13.273 16242 Z= 0.281 Chirality : 0.042 0.151 1852 Planarity : 0.004 0.039 2058 Dihedral : 4.265 19.707 1662 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.98 % Allowed : 15.61 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.11 (0.22), residues: 1522 helix: 1.62 (0.20), residues: 662 sheet: -1.31 (0.42), residues: 164 loop : -1.10 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 435 TYR 0.021 0.001 TYR A 629 PHE 0.022 0.001 PHE A 712 TRP 0.020 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (11918) covalent geometry : angle 0.55610 / 0.28 (16210) SS BOND : bond 0.00240 / 0.16 ( 16) SS BOND : angle 0.84010 / 0.52 ( 32) hydrogen bonds : bond 0.04135 / 2.79 ( 527) hydrogen bonds : angle 3.71717 / 2.54 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.7958 (mmp) cc_final: 0.7716 (mmp) REVERT: B 494 MET cc_start: 0.9374 (ttt) cc_final: 0.9126 (ttt) REVERT: B 601 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6702 (t80) REVERT: B 688 MET cc_start: 0.6638 (mmt) cc_final: 0.6257 (mmt) REVERT: A 79 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7818 (tt) REVERT: A 494 MET cc_start: 0.9357 (ttt) cc_final: 0.9110 (ttt) REVERT: A 601 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6702 (t80) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.0844 time to fit residues: 18.8827 Evaluate side-chains 143 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 788 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 142 optimal weight: 0.0870 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120292 restraints weight = 22073.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119256 restraints weight = 16829.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120174 restraints weight = 18185.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120547 restraints weight = 13706.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121058 restraints weight = 12939.558| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11934 Z= 0.100 Angle : 0.515 12.275 16242 Z= 0.258 Chirality : 0.040 0.140 1852 Planarity : 0.003 0.030 2058 Dihedral : 3.943 18.720 1662 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.32 % Allowed : 16.35 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: 0.32 (0.22), residues: 1522 helix: 1.71 (0.20), residues: 668 sheet: -1.02 (0.44), residues: 152 loop : -0.99 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 435 TYR 0.019 0.001 TYR A 629 PHE 0.021 0.001 PHE A 768 TRP 0.016 0.001 TRP A 575 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (11918) covalent geometry : angle 0.51495 / 0.26 (16210) SS BOND : bond 0.00184 / 0.12 ( 16) SS BOND : angle 0.72948 / 0.47 ( 32) hydrogen bonds : bond 0.03295 / 2.24 ( 527) hydrogen bonds : angle 3.52243 / 2.42 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1682.35 seconds wall clock time: 29 minutes 45.52 seconds (1785.52 seconds total)