Starting phenix.real_space_refine on Mon Dec 30 20:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy8_42795/12_2024/8uy8_42795.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 76 5.16 5 C 8826 2.51 5 N 2348 2.21 5 O 2671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13927 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 6926 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 43, 'TRANS': 856} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 6845 Classifications: {'peptide': 894} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 43, 'TRANS': 850} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Time building chain proxies: 9.30, per 1000 atoms: 0.67 Number of scatterers: 13927 At special positions: 0 Unit cell: (105.41, 129.48, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Mg 6 11.99 O 2671 8.00 N 2348 7.00 C 8826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 54.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.606A pdb=" N HIS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 4.133A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.101A pdb=" N GLN A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.529A pdb=" N LEU A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 153 removed outlier: 3.578A pdb=" N VAL A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.624A pdb=" N CYS A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 279 through 312 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 313 through 326 removed outlier: 3.918A pdb=" N LEU A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.025A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.746A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.712A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.829A pdb=" N VAL A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.589A pdb=" N GLU A 532 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.680A pdb=" N GLU A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 597' Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.753A pdb=" N GLN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 629 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 677 through 717 Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 763 through 773 removed outlier: 3.644A pdb=" N ARG A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 777 through 790 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.742A pdb=" N PHE A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.805A pdb=" N SER A 858 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 4.200A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.661A pdb=" N THR B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 57' Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 120 through 153 removed outlier: 3.845A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 279 through 312 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.881A pdb=" N LEU B 319 " --> pdb=" O TRP B 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 350 removed outlier: 4.116A pdb=" N MET B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.703A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.704A pdb=" N LEU B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.797A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.574A pdb=" N GLU B 532 " --> pdb=" O ARG B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 600 through 611 removed outlier: 3.793A pdb=" N GLN B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 629 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 677 through 716 removed outlier: 3.586A pdb=" N LEU B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 762 through 773 removed outlier: 4.322A pdb=" N GLY B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 790 removed outlier: 3.798A pdb=" N PHE B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 798 through 817 removed outlier: 4.252A pdb=" N PHE B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 809 " --> pdb=" O GLY B 805 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 814 " --> pdb=" O GLY B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.598A pdb=" N SER B 858 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 4.257A pdb=" N TRP B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.684A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 245 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE A 206 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 249 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 204 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA A 251 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 202 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 253 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 200 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 255 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG A 198 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 205 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.684A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 245 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE A 206 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 249 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 204 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA A 251 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 202 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 253 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 200 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 255 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG A 198 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.621A pdb=" N GLY A 655 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU A 673 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 657 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 636 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE A 656 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 638 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N VAL A 658 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 370 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 568 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR A 372 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.813A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 515 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR A 540 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 513 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 542 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 511 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 457 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 439 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.813A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N CYS A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 537 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N ARG A 482 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 12.575A pdb=" N ILE A 541 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.695A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.695A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS B 240 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.621A pdb=" N GLY B 655 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU B 673 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER B 657 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 636 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 656 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 638 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL B 658 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.922A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 515 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR B 540 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 513 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 542 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG B 511 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER B 453 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU B 442 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 455 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.922A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N CYS B 478 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 537 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ARG B 482 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 12.470A pdb=" N ILE B 541 " --> pdb=" O ARG B 482 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2229 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: 5.98 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2291 1.31 - 1.43: 3503 1.43 - 1.56: 8132 1.56 - 1.68: 0 1.68 - 1.81: 132 Bond restraints: 14058 Sorted by residual: bond pdb=" C THR A 702 " pdb=" O THR A 702 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.26e-02 6.30e+03 1.65e+01 bond pdb=" C MET A 701 " pdb=" O MET A 701 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.49e+01 bond pdb=" CA ARG A 20 " pdb=" C ARG A 20 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.33e-02 5.65e+03 1.21e+01 bond pdb=" C ILE A 778 " pdb=" O ILE A 778 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.13e-02 7.83e+03 1.12e+01 bond pdb=" CA THR A 702 " pdb=" C THR A 702 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.35e-02 5.49e+03 1.02e+01 ... (remaining 14053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18786 1.93 - 3.86: 305 3.86 - 5.80: 44 5.80 - 7.73: 11 7.73 - 9.66: 3 Bond angle restraints: 19149 Sorted by residual: angle pdb=" N SER A 777 " pdb=" CA SER A 777 " pdb=" C SER A 777 " ideal model delta sigma weight residual 113.41 103.75 9.66 1.22e+00 6.72e-01 6.27e+01 angle pdb=" N PRO A 35 " pdb=" CA PRO A 35 " pdb=" C PRO A 35 " ideal model delta sigma weight residual 110.70 102.69 8.01 1.22e+00 6.72e-01 4.31e+01 angle pdb=" N ILE A 163 " pdb=" CA ILE A 163 " pdb=" C ILE A 163 " ideal model delta sigma weight residual 110.72 116.18 -5.46 1.01e+00 9.80e-01 2.92e+01 angle pdb=" N ILE A 699 " pdb=" CA ILE A 699 " pdb=" C ILE A 699 " ideal model delta sigma weight residual 110.72 115.62 -4.90 1.01e+00 9.80e-01 2.35e+01 angle pdb=" CA GLU A 273 " pdb=" C GLU A 273 " pdb=" N GLN A 274 " ideal model delta sigma weight residual 119.52 115.97 3.55 7.90e-01 1.60e+00 2.02e+01 ... (remaining 19144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7716 16.84 - 33.68: 597 33.68 - 50.52: 114 50.52 - 67.36: 16 67.36 - 84.20: 10 Dihedral angle restraints: 8453 sinusoidal: 3254 harmonic: 5199 Sorted by residual: dihedral pdb=" CA ASN B 164 " pdb=" C ASN B 164 " pdb=" N ASP B 165 " pdb=" CA ASP B 165 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CA ARG A 270 " pdb=" CB ARG A 270 " ideal model delta harmonic sigma weight residual 122.80 132.26 -9.46 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" N LEU A 267 " pdb=" C LEU A 267 " pdb=" CA LEU A 267 " pdb=" CB LEU A 267 " ideal model delta harmonic sigma weight residual 122.80 132.25 -9.45 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 8450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2080 0.077 - 0.153: 182 0.153 - 0.230: 4 0.230 - 0.306: 3 0.306 - 0.383: 3 Chirality restraints: 2272 Sorted by residual: chirality pdb=" CA LEU A 267 " pdb=" N LEU A 267 " pdb=" C LEU A 267 " pdb=" CB LEU A 267 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ARG A 270 " pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CB ARG A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA GLN A 27 " pdb=" N GLN A 27 " pdb=" C GLN A 27 " pdb=" CB GLN A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2269 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 262 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C THR A 262 " 0.045 2.00e-02 2.50e+03 pdb=" O THR A 262 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP A 263 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 488 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO B 489 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 489 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 489 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 170 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLY A 170 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 170 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP A 171 " -0.014 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 141 2.59 - 3.17: 11583 3.17 - 3.74: 22071 3.74 - 4.32: 30191 4.32 - 4.90: 51518 Nonbonded interactions: 115504 Sorted by model distance: nonbonded pdb=" OD1 ASN B 709 " pdb="MG MG B1001 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASN A 709 " pdb="MG MG A1001 " model vdw 2.041 2.170 nonbonded pdb=" OD1 ASP A 204 " pdb="MG MG A1003 " model vdw 2.116 2.170 nonbonded pdb=" OD1 ASP B 191 " pdb="MG MG B1002 " model vdw 2.164 2.170 nonbonded pdb=" OD1 ASP B 426 " pdb=" OG SER B 429 " model vdw 2.232 3.040 ... (remaining 115499 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 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 163 or (resid 164 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 through 892 or (re \ sid 893 through 895 and (name N or name CA or name C or name O or name CB )) or \ resid 896 or resid 1001 through 1003)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.580 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 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 : 0.004 0.061 14058 Z= 0.236 Angle : 0.620 9.661 19149 Z= 0.360 Chirality : 0.045 0.383 2272 Planarity : 0.005 0.063 2439 Dihedral : 12.757 84.203 5073 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1790 helix: 1.34 (0.18), residues: 890 sheet: -0.14 (0.34), residues: 174 loop : -0.69 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 171 HIS 0.004 0.001 HIS B 357 PHE 0.022 0.001 PHE A 364 TYR 0.033 0.001 TYR B 698 ARG 0.004 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.597 Fit side-chains REVERT: A 49 PRO cc_start: 0.8762 (Cg_exo) cc_final: 0.8549 (Cg_endo) REVERT: A 133 LEU cc_start: 0.7971 (mp) cc_final: 0.7632 (tp) REVERT: A 137 ILE cc_start: 0.8736 (mt) cc_final: 0.8516 (mp) REVERT: A 144 LYS cc_start: 0.8140 (tttm) cc_final: 0.7435 (mttp) REVERT: A 242 MET cc_start: 0.8789 (ttt) cc_final: 0.8543 (ttp) REVERT: A 620 MET cc_start: 0.8475 (mmp) cc_final: 0.7772 (tpt) REVERT: A 756 LYS cc_start: 0.8829 (mttt) cc_final: 0.8518 (mtpp) REVERT: A 764 ASP cc_start: 0.8009 (t0) cc_final: 0.7732 (t70) REVERT: A 787 MET cc_start: 0.9080 (mmm) cc_final: 0.8832 (mmm) REVERT: B 98 ARG cc_start: 0.7751 (ptt180) cc_final: 0.7502 (ptm160) REVERT: B 479 SER cc_start: 0.9154 (t) cc_final: 0.8876 (p) REVERT: B 824 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7404 (tpp-160) REVERT: B 867 LEU cc_start: 0.7921 (tt) cc_final: 0.7616 (mm) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.3021 time to fit residues: 116.6789 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.0370 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN B 60 HIS B 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14058 Z= 0.287 Angle : 0.576 9.008 19149 Z= 0.294 Chirality : 0.043 0.159 2272 Planarity : 0.005 0.055 2439 Dihedral : 4.252 29.843 1902 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.09 % Allowed : 7.69 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1790 helix: 1.60 (0.18), residues: 906 sheet: -0.19 (0.35), residues: 170 loop : -0.64 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 806 HIS 0.004 0.001 HIS B 357 PHE 0.029 0.002 PHE A 364 TYR 0.029 0.001 TYR B 698 ARG 0.006 0.001 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8043 (tttm) cc_final: 0.7312 (mttp) REVERT: A 226 ARG cc_start: 0.8586 (ptp90) cc_final: 0.8244 (ptp90) REVERT: A 242 MET cc_start: 0.8811 (ttt) cc_final: 0.8602 (ttp) REVERT: A 299 MET cc_start: 0.8477 (mtp) cc_final: 0.8047 (mtp) REVERT: A 620 MET cc_start: 0.8514 (mmp) cc_final: 0.7793 (tpt) REVERT: A 756 LYS cc_start: 0.8853 (mttt) cc_final: 0.8647 (mtpp) REVERT: A 787 MET cc_start: 0.9048 (mmm) cc_final: 0.8787 (mmm) REVERT: B 98 ARG cc_start: 0.7846 (ptt180) cc_final: 0.7551 (ptm160) REVERT: B 394 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7591 (ttpp) REVERT: B 549 GLU cc_start: 0.8601 (pm20) cc_final: 0.8336 (pm20) REVERT: B 820 MET cc_start: 0.8827 (mmt) cc_final: 0.8604 (mmm) REVERT: B 824 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7458 (tpp-160) REVERT: B 867 LEU cc_start: 0.7846 (tt) cc_final: 0.7534 (mm) outliers start: 16 outliers final: 7 residues processed: 161 average time/residue: 0.3118 time to fit residues: 73.0384 Evaluate side-chains 136 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 863 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN B 282 GLN B 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14058 Z= 0.247 Angle : 0.528 6.896 19149 Z= 0.271 Chirality : 0.042 0.149 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.156 27.514 1902 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.09 % Allowed : 9.39 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1790 helix: 1.73 (0.18), residues: 901 sheet: -0.32 (0.35), residues: 178 loop : -0.63 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.004 0.001 HIS B 357 PHE 0.020 0.001 PHE A 364 TYR 0.017 0.001 TYR B 698 ARG 0.005 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8041 (tttm) cc_final: 0.7308 (mttp) REVERT: A 242 MET cc_start: 0.8820 (ttt) cc_final: 0.8609 (ttp) REVERT: A 299 MET cc_start: 0.8425 (mtp) cc_final: 0.7962 (mtp) REVERT: A 359 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.9122 (p0) REVERT: A 620 MET cc_start: 0.8536 (mmp) cc_final: 0.7762 (tpt) REVERT: A 728 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 756 LYS cc_start: 0.8861 (mttt) cc_final: 0.8529 (mtpp) REVERT: B 98 ARG cc_start: 0.7841 (ptt180) cc_final: 0.7588 (ptm160) REVERT: B 394 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7600 (ttpp) REVERT: B 549 GLU cc_start: 0.8669 (pm20) cc_final: 0.8368 (pm20) REVERT: B 820 MET cc_start: 0.8819 (mmt) cc_final: 0.8457 (mmm) REVERT: B 867 LEU cc_start: 0.7856 (tt) cc_final: 0.7557 (mm) outliers start: 16 outliers final: 6 residues processed: 152 average time/residue: 0.2947 time to fit residues: 65.3097 Evaluate side-chains 138 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14058 Z= 0.203 Angle : 0.508 8.134 19149 Z= 0.258 Chirality : 0.041 0.146 2272 Planarity : 0.005 0.052 2439 Dihedral : 3.993 18.222 1900 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 10.28 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1790 helix: 1.86 (0.18), residues: 898 sheet: -0.29 (0.34), residues: 194 loop : -0.54 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.004 0.001 HIS B 357 PHE 0.014 0.001 PHE A 364 TYR 0.016 0.001 TYR B 869 ARG 0.004 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8053 (tttm) cc_final: 0.7320 (mttp) REVERT: A 242 MET cc_start: 0.8796 (ttt) cc_final: 0.8588 (ttp) REVERT: A 359 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.9115 (p0) REVERT: A 620 MET cc_start: 0.8555 (mmp) cc_final: 0.7772 (tpt) REVERT: A 728 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 756 LYS cc_start: 0.8864 (mttt) cc_final: 0.8506 (mtpp) REVERT: B 62 GLU cc_start: 0.8267 (mp0) cc_final: 0.7713 (pm20) REVERT: B 98 ARG cc_start: 0.7823 (ptt180) cc_final: 0.7567 (ptm160) REVERT: B 394 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7578 (ttpp) REVERT: B 549 GLU cc_start: 0.8697 (pm20) cc_final: 0.8359 (pm20) REVERT: B 867 LEU cc_start: 0.7826 (tt) cc_final: 0.7533 (mm) outliers start: 22 outliers final: 9 residues processed: 160 average time/residue: 0.2898 time to fit residues: 67.9414 Evaluate side-chains 142 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14058 Z= 0.245 Angle : 0.522 8.229 19149 Z= 0.265 Chirality : 0.041 0.150 2272 Planarity : 0.004 0.051 2439 Dihedral : 4.002 17.427 1900 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.43 % Allowed : 10.96 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1790 helix: 1.80 (0.18), residues: 906 sheet: -0.28 (0.34), residues: 194 loop : -0.57 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.004 0.001 HIS B 357 PHE 0.013 0.001 PHE A 364 TYR 0.019 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8047 (tttm) cc_final: 0.7308 (mttp) REVERT: A 242 MET cc_start: 0.8824 (ttt) cc_final: 0.8612 (ttp) REVERT: A 299 MET cc_start: 0.8428 (mtp) cc_final: 0.8002 (mtp) REVERT: A 359 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.9131 (p0) REVERT: A 756 LYS cc_start: 0.8855 (mttt) cc_final: 0.8499 (mtpp) REVERT: B 98 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7575 (ptm160) REVERT: B 394 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7564 (ttpp) REVERT: B 549 GLU cc_start: 0.8727 (pm20) cc_final: 0.8374 (pm20) REVERT: B 867 LEU cc_start: 0.7828 (tt) cc_final: 0.7541 (mm) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.2877 time to fit residues: 64.6849 Evaluate side-chains 144 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.0170 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14058 Z= 0.228 Angle : 0.527 11.166 19149 Z= 0.265 Chirality : 0.041 0.147 2272 Planarity : 0.004 0.051 2439 Dihedral : 3.982 16.554 1900 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.57 % Allowed : 11.30 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1790 helix: 1.86 (0.18), residues: 906 sheet: -0.27 (0.34), residues: 188 loop : -0.56 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.004 0.001 HIS B 357 PHE 0.012 0.001 PHE A 779 TYR 0.019 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8042 (tttm) cc_final: 0.7306 (mttp) REVERT: A 242 MET cc_start: 0.8827 (ttt) cc_final: 0.8618 (ttt) REVERT: A 299 MET cc_start: 0.8445 (mtp) cc_final: 0.8028 (mtp) REVERT: A 359 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.9123 (p0) REVERT: A 756 LYS cc_start: 0.8849 (mttt) cc_final: 0.8491 (mtpp) REVERT: B 62 GLU cc_start: 0.8294 (mp0) cc_final: 0.7751 (pm20) REVERT: B 98 ARG cc_start: 0.7862 (ptt180) cc_final: 0.7588 (ptm160) REVERT: B 394 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7563 (ttpp) REVERT: B 483 HIS cc_start: 0.8399 (t-170) cc_final: 0.8101 (t-170) REVERT: B 549 GLU cc_start: 0.8749 (pm20) cc_final: 0.8402 (pm20) REVERT: B 667 GLU cc_start: 0.8709 (tp30) cc_final: 0.8314 (tp30) REVERT: B 867 LEU cc_start: 0.7853 (tt) cc_final: 0.7565 (mm) outliers start: 23 outliers final: 19 residues processed: 154 average time/residue: 0.2875 time to fit residues: 65.6853 Evaluate side-chains 150 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 172 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14058 Z= 0.183 Angle : 0.515 10.264 19149 Z= 0.258 Chirality : 0.040 0.144 2272 Planarity : 0.004 0.052 2439 Dihedral : 3.906 15.786 1900 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 1.36 % Allowed : 12.05 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1790 helix: 1.96 (0.18), residues: 906 sheet: -0.30 (0.33), residues: 200 loop : -0.52 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE A 779 TYR 0.022 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8756 (mt) cc_final: 0.8450 (mt) REVERT: A 144 LYS cc_start: 0.8061 (tttm) cc_final: 0.7317 (mttp) REVERT: A 242 MET cc_start: 0.8816 (ttt) cc_final: 0.8575 (ttp) REVERT: A 266 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7647 (pp30) REVERT: A 299 MET cc_start: 0.8400 (mtp) cc_final: 0.7963 (mtp) REVERT: A 359 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9103 (p0) REVERT: A 756 LYS cc_start: 0.8844 (mttt) cc_final: 0.8491 (mtpp) REVERT: A 845 MET cc_start: 0.8429 (mmm) cc_final: 0.7949 (mmt) REVERT: B 62 GLU cc_start: 0.8303 (mp0) cc_final: 0.7774 (pm20) REVERT: B 98 ARG cc_start: 0.7838 (ptt180) cc_final: 0.7565 (ptm160) REVERT: B 394 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7556 (ttpp) REVERT: B 483 HIS cc_start: 0.8371 (t-170) cc_final: 0.8086 (t-170) REVERT: B 549 GLU cc_start: 0.8767 (pm20) cc_final: 0.8410 (pm20) REVERT: B 667 GLU cc_start: 0.8676 (tp30) cc_final: 0.8280 (tp30) REVERT: B 867 LEU cc_start: 0.7828 (tt) cc_final: 0.7543 (mm) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.2893 time to fit residues: 66.9378 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.0020 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14058 Z= 0.194 Angle : 0.514 11.890 19149 Z= 0.259 Chirality : 0.041 0.181 2272 Planarity : 0.004 0.053 2439 Dihedral : 3.887 14.995 1900 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.63 % Allowed : 12.66 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1790 helix: 1.97 (0.18), residues: 906 sheet: -0.30 (0.33), residues: 200 loop : -0.50 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.006 0.001 HIS B 357 PHE 0.011 0.001 PHE A 779 TYR 0.022 0.001 TYR B 869 ARG 0.005 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8757 (mt) cc_final: 0.8444 (mt) REVERT: A 144 LYS cc_start: 0.8064 (tttm) cc_final: 0.7317 (mttp) REVERT: A 242 MET cc_start: 0.8817 (ttt) cc_final: 0.8595 (ttp) REVERT: A 266 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (pp30) REVERT: A 299 MET cc_start: 0.8393 (mtp) cc_final: 0.7958 (mtp) REVERT: A 359 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9106 (p0) REVERT: A 756 LYS cc_start: 0.8846 (mttt) cc_final: 0.8495 (mtpp) REVERT: A 845 MET cc_start: 0.8427 (mmm) cc_final: 0.7947 (mmt) REVERT: B 62 GLU cc_start: 0.8309 (mp0) cc_final: 0.8052 (pm20) REVERT: B 98 ARG cc_start: 0.7836 (ptt180) cc_final: 0.7562 (ptm160) REVERT: B 394 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7556 (ttpp) REVERT: B 427 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 431 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8137 (mtm110) REVERT: B 483 HIS cc_start: 0.8371 (t-170) cc_final: 0.8076 (t-170) REVERT: B 549 GLU cc_start: 0.8766 (pm20) cc_final: 0.8409 (pm20) REVERT: B 667 GLU cc_start: 0.8678 (tp30) cc_final: 0.8308 (tp30) REVERT: B 787 MET cc_start: 0.8652 (mmp) cc_final: 0.8029 (mmt) REVERT: B 867 LEU cc_start: 0.7825 (tt) cc_final: 0.7539 (mm) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.2776 time to fit residues: 64.1354 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14058 Z= 0.206 Angle : 0.522 12.088 19149 Z= 0.261 Chirality : 0.041 0.172 2272 Planarity : 0.004 0.053 2439 Dihedral : 3.902 14.590 1900 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 1.63 % Allowed : 12.46 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1790 helix: 2.03 (0.18), residues: 898 sheet: -0.27 (0.33), residues: 199 loop : -0.44 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 789 HIS 0.006 0.001 HIS B 357 PHE 0.011 0.001 PHE A 779 TYR 0.012 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8045 (tttm) cc_final: 0.7303 (mttp) REVERT: A 242 MET cc_start: 0.8831 (ttt) cc_final: 0.8601 (ttt) REVERT: A 299 MET cc_start: 0.8398 (mtp) cc_final: 0.7959 (mtp) REVERT: A 359 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9107 (p0) REVERT: A 756 LYS cc_start: 0.8842 (mttt) cc_final: 0.8491 (mtpp) REVERT: B 62 GLU cc_start: 0.8298 (mp0) cc_final: 0.8047 (pm20) REVERT: B 98 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7577 (ptm160) REVERT: B 394 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7556 (ttpp) REVERT: B 431 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8202 (mtm110) REVERT: B 483 HIS cc_start: 0.8354 (t-170) cc_final: 0.8088 (t-170) REVERT: B 549 GLU cc_start: 0.8769 (pm20) cc_final: 0.8406 (pm20) REVERT: B 667 GLU cc_start: 0.8682 (tp30) cc_final: 0.8324 (tp30) REVERT: B 867 LEU cc_start: 0.7814 (tt) cc_final: 0.7529 (mm) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 0.2658 time to fit residues: 61.1191 Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14058 Z= 0.275 Angle : 0.559 12.303 19149 Z= 0.279 Chirality : 0.042 0.171 2272 Planarity : 0.005 0.053 2439 Dihedral : 4.028 15.128 1900 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 1.50 % Allowed : 13.14 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1790 helix: 1.91 (0.18), residues: 898 sheet: -0.26 (0.34), residues: 187 loop : -0.49 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 263 HIS 0.006 0.001 HIS B 357 PHE 0.013 0.001 PHE A 779 TYR 0.014 0.001 TYR A 869 ARG 0.004 0.000 ARG B 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8859 (ttt) cc_final: 0.8622 (ttt) REVERT: A 299 MET cc_start: 0.8405 (mtp) cc_final: 0.7977 (mtp) REVERT: A 756 LYS cc_start: 0.8854 (mttt) cc_final: 0.8494 (mtpp) REVERT: A 845 MET cc_start: 0.8437 (mmm) cc_final: 0.8121 (mmm) REVERT: B 62 GLU cc_start: 0.8330 (mp0) cc_final: 0.8069 (pm20) REVERT: B 98 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7603 (ptm160) REVERT: B 394 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7549 (ttpp) REVERT: B 431 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8284 (mtm110) REVERT: B 549 GLU cc_start: 0.8751 (pm20) cc_final: 0.8387 (pm20) REVERT: B 867 LEU cc_start: 0.7822 (tt) cc_final: 0.7550 (mm) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.2927 time to fit residues: 64.3542 Evaluate side-chains 149 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 863 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.084556 restraints weight = 20009.455| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.25 r_work: 0.2839 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 14058 Z= 0.327 Angle : 0.810 59.189 19149 Z= 0.459 Chirality : 0.043 0.623 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.029 15.119 1900 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.29 % Allowed : 13.41 % Favored : 85.30 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1790 helix: 1.91 (0.18), residues: 898 sheet: -0.26 (0.34), residues: 187 loop : -0.49 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 263 HIS 0.006 0.001 HIS B 357 PHE 0.013 0.001 PHE A 779 TYR 0.013 0.001 TYR A 869 ARG 0.003 0.000 ARG B 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.10 seconds wall clock time: 58 minutes 35.40 seconds (3515.40 seconds total)