Starting phenix.real_space_refine on Fri May 16 03:48:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy8_42795/05_2025/8uy8_42795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy8_42795/05_2025/8uy8_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_42795/05_2025/8uy8_42795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy8_42795/05_2025/8uy8_42795.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy8_42795/05_2025/8uy8_42795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy8_42795/05_2025/8uy8_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-5687/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: 9.54, per 1000 atoms: 0.69 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 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: 1.86 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: 5.55 Time building geometry restraints manager: 4.45 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: 6.470 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.400 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.030 ------------------------------------------------------------------------------- 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= 0.205 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 Details of bonding type rmsd hydrogen bonds : bond 0.12990 ( 734) hydrogen bonds : angle 6.29391 ( 2229) covalent geometry : bond 0.00353 (14058) covalent geometry : angle 0.61961 (19149) *********************** 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 : 1.510 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: 0.3122 time to fit residues: 120.8416 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 : 1.510 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.085188 restraints weight = 20172.817| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.27 r_work: 0.2851 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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= 0.179 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 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 734) hydrogen bonds : angle 4.63165 ( 2229) covalent geometry : bond 0.00435 (14058) covalent geometry : angle 0.57629 (19149) *********************** 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 : 1.640 Fit side-chains revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6507 (ptp-110) cc_final: 0.6279 (ptm160) REVERT: A 144 LYS cc_start: 0.8147 (tttm) cc_final: 0.7379 (mttp) REVERT: A 226 ARG cc_start: 0.8497 (ptp90) cc_final: 0.8143 (ptp90) REVERT: A 299 MET cc_start: 0.8470 (mtp) cc_final: 0.8042 (mtp) REVERT: A 620 MET cc_start: 0.8795 (mmp) cc_final: 0.7883 (tpt) REVERT: A 787 MET cc_start: 0.9074 (mmm) cc_final: 0.8808 (mmm) REVERT: B 98 ARG cc_start: 0.8107 (ptt180) cc_final: 0.7667 (ptm160) REVERT: B 394 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7605 (ttpp) REVERT: B 549 GLU cc_start: 0.8551 (pm20) cc_final: 0.8287 (pm20) REVERT: B 820 MET cc_start: 0.8870 (mmt) cc_final: 0.8637 (mmm) REVERT: B 824 ARG cc_start: 0.8619 (tpp80) cc_final: 0.7692 (tpp-160) REVERT: B 867 LEU cc_start: 0.7833 (tt) cc_final: 0.7511 (mm) outliers start: 16 outliers final: 7 residues processed: 161 average time/residue: 0.2804 time to fit residues: 65.5558 Evaluate side-chains 135 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.086427 restraints weight = 20301.451| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.30 r_work: 0.2861 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14058 Z= 0.134 Angle : 0.515 6.702 19149 Z= 0.264 Chirality : 0.041 0.146 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.110 27.363 1902 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 0.88 % Allowed : 9.33 % Favored : 89.79 % 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: 0.93 (0.20), residues: 1790 helix: 1.79 (0.18), residues: 901 sheet: -0.34 (0.34), residues: 188 loop : -0.62 (0.23), residues: 701 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 0.018 0.001 PHE A 364 TYR 0.014 0.001 TYR B 698 ARG 0.004 0.000 ARG B 650 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 734) hydrogen bonds : angle 4.39282 ( 2229) covalent geometry : bond 0.00318 (14058) covalent geometry : angle 0.51545 (19149) *********************** 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 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8144 (tttm) cc_final: 0.7393 (mttp) REVERT: A 299 MET cc_start: 0.8401 (mtp) cc_final: 0.7934 (mtp) REVERT: A 359 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8990 (p0) REVERT: A 620 MET cc_start: 0.8773 (mmp) cc_final: 0.7830 (tpt) REVERT: A 728 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7923 (tp) REVERT: A 787 MET cc_start: 0.9053 (mmm) cc_final: 0.8813 (mmm) REVERT: B 98 ARG cc_start: 0.8083 (ptt180) cc_final: 0.7642 (ptm160) REVERT: B 394 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7561 (ttpp) REVERT: B 549 GLU cc_start: 0.8618 (pm20) cc_final: 0.8325 (pm20) REVERT: B 820 MET cc_start: 0.8843 (mmt) cc_final: 0.8472 (mmm) REVERT: B 867 LEU cc_start: 0.7832 (tt) cc_final: 0.7527 (mm) outliers start: 13 outliers final: 5 residues processed: 149 average time/residue: 0.2823 time to fit residues: 60.6014 Evaluate side-chains 135 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP 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 137 optimal weight: 0.3980 chunk 178 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.115145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.086575 restraints weight = 20284.565| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.30 r_work: 0.2873 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1930 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= 0.127 Angle : 0.505 8.228 19149 Z= 0.257 Chirality : 0.041 0.144 2272 Planarity : 0.004 0.052 2439 Dihedral : 3.957 18.128 1900 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.70 % Allowed : 9.94 % Favored : 88.36 % 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: 1.07 (0.20), residues: 1790 helix: 1.89 (0.18), residues: 898 sheet: -0.30 (0.33), residues: 208 loop : -0.51 (0.23), residues: 684 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 0.015 0.001 PHE A 364 TYR 0.016 0.001 TYR B 869 ARG 0.003 0.000 ARG A 822 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 734) hydrogen bonds : angle 4.25683 ( 2229) covalent geometry : bond 0.00303 (14058) covalent geometry : angle 0.50521 (19149) *********************** 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 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8160 (tttm) cc_final: 0.7394 (mttp) REVERT: A 359 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8977 (p0) REVERT: A 620 MET cc_start: 0.8806 (mmp) cc_final: 0.7823 (tpt) REVERT: A 728 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7909 (tt) REVERT: B 62 GLU cc_start: 0.8412 (mp0) cc_final: 0.7827 (pm20) REVERT: B 98 ARG cc_start: 0.8052 (ptt180) cc_final: 0.7649 (ptm160) REVERT: B 394 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7520 (ttpp) REVERT: B 549 GLU cc_start: 0.8638 (pm20) cc_final: 0.8298 (pm20) REVERT: B 867 LEU cc_start: 0.7790 (tt) cc_final: 0.7486 (mm) outliers start: 25 outliers final: 10 residues processed: 163 average time/residue: 0.2608 time to fit residues: 63.2095 Evaluate side-chains 141 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 842 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 A 900 HIS B 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085411 restraints weight = 20281.078| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.29 r_work: 0.2857 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2023 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= 0.150 Angle : 0.520 8.205 19149 Z= 0.263 Chirality : 0.041 0.148 2272 Planarity : 0.004 0.051 2439 Dihedral : 3.971 17.391 1900 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.29 % Allowed : 11.10 % 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: 1.04 (0.20), residues: 1790 helix: 1.85 (0.18), residues: 906 sheet: -0.26 (0.34), residues: 194 loop : -0.56 (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 0.014 0.001 PHE A 364 TYR 0.019 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 734) hydrogen bonds : angle 4.25743 ( 2229) covalent geometry : bond 0.00365 (14058) covalent geometry : angle 0.52005 (19149) *********************** 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 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8143 (tttm) cc_final: 0.7368 (mttp) REVERT: A 299 MET cc_start: 0.8422 (mtp) cc_final: 0.8001 (mtp) REVERT: A 359 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.9006 (p0) REVERT: B 98 ARG cc_start: 0.8101 (ptt180) cc_final: 0.7668 (ptm160) REVERT: B 394 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7562 (ttpp) REVERT: B 549 GLU cc_start: 0.8688 (pm20) cc_final: 0.8326 (pm20) REVERT: B 867 LEU cc_start: 0.7794 (tt) cc_final: 0.7504 (mm) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.2670 time to fit residues: 58.9609 Evaluate side-chains 142 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 842 VAL 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 141 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 165 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.083682 restraints weight = 20339.606| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.27 r_work: 0.2833 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14058 Z= 0.196 Angle : 0.562 10.973 19149 Z= 0.283 Chirality : 0.043 0.153 2272 Planarity : 0.005 0.051 2439 Dihedral : 4.079 16.692 1900 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.63 % Allowed : 11.23 % 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: 0.92 (0.20), residues: 1790 helix: 1.74 (0.18), residues: 905 sheet: -0.35 (0.33), residues: 194 loop : -0.58 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.011 0.001 HIS A 899 PHE 0.013 0.001 PHE A 779 TYR 0.021 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 734) hydrogen bonds : angle 4.33073 ( 2229) covalent geometry : bond 0.00482 (14058) covalent geometry : angle 0.56159 (19149) *********************** 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 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8457 (mtp) cc_final: 0.8046 (mtp) REVERT: B 62 GLU cc_start: 0.8455 (mp0) cc_final: 0.7875 (pm20) REVERT: B 98 ARG cc_start: 0.8167 (ptt180) cc_final: 0.7714 (ptm160) REVERT: B 394 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7582 (ttpp) REVERT: B 549 GLU cc_start: 0.8712 (pm20) cc_final: 0.8355 (pm20) REVERT: B 867 LEU cc_start: 0.7890 (tt) cc_final: 0.7585 (mm) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.2697 time to fit residues: 58.9006 Evaluate side-chains 142 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 254 MET 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 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 A 900 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.085306 restraints weight = 20250.360| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.26 r_work: 0.2857 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14058 Z= 0.136 Angle : 0.531 10.558 19149 Z= 0.266 Chirality : 0.041 0.147 2272 Planarity : 0.004 0.052 2439 Dihedral : 3.992 15.934 1900 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.29 % Allowed : 12.25 % Favored : 86.45 % 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: 1.08 (0.20), residues: 1790 helix: 1.91 (0.18), residues: 898 sheet: -0.33 (0.34), residues: 188 loop : -0.53 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.005 0.001 HIS B 357 PHE 0.012 0.001 PHE A 779 TYR 0.024 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 734) hydrogen bonds : angle 4.23849 ( 2229) covalent geometry : bond 0.00327 (14058) covalent geometry : angle 0.53119 (19149) *********************** 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 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: A 299 MET cc_start: 0.8402 (mtp) cc_final: 0.7987 (mtp) REVERT: B 98 ARG cc_start: 0.8114 (ptt180) cc_final: 0.7680 (ptm160) REVERT: B 394 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7565 (ttpp) REVERT: B 549 GLU cc_start: 0.8720 (pm20) cc_final: 0.8331 (pm20) REVERT: B 667 GLU cc_start: 0.8936 (tp30) cc_final: 0.8578 (tp30) REVERT: B 670 ASP cc_start: 0.9253 (m-30) cc_final: 0.9043 (m-30) REVERT: B 820 MET cc_start: 0.8761 (mmm) cc_final: 0.8535 (mmt) REVERT: B 867 LEU cc_start: 0.7822 (tt) cc_final: 0.7524 (mm) outliers start: 19 outliers final: 17 residues processed: 147 average time/residue: 0.2586 time to fit residues: 56.0291 Evaluate side-chains 147 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 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 254 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 0.0030 chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 86 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.2604 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087956 restraints weight = 20039.251| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.26 r_work: 0.2894 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14058 Z= 0.097 Angle : 0.499 9.819 19149 Z= 0.253 Chirality : 0.040 0.150 2272 Planarity : 0.004 0.056 2439 Dihedral : 3.815 14.964 1900 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 12.80 % 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: 1.28 (0.20), residues: 1790 helix: 2.11 (0.18), residues: 898 sheet: -0.34 (0.33), residues: 200 loop : -0.43 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 789 HIS 0.021 0.001 HIS A 899 PHE 0.009 0.001 PHE A 779 TYR 0.024 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 734) hydrogen bonds : angle 4.10142 ( 2229) covalent geometry : bond 0.00214 (14058) covalent geometry : angle 0.49920 (19149) *********************** 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 159 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8182 (ptmm) REVERT: A 299 MET cc_start: 0.8382 (mtp) cc_final: 0.7955 (mtp) REVERT: A 845 MET cc_start: 0.8436 (mmm) cc_final: 0.8210 (mmm) REVERT: B 62 GLU cc_start: 0.8432 (mp0) cc_final: 0.7867 (pm20) REVERT: B 98 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7619 (ptm160) REVERT: B 394 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7531 (ttpp) REVERT: B 427 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8385 (tm-30) REVERT: B 483 HIS cc_start: 0.8420 (t-170) cc_final: 0.8139 (t-170) REVERT: B 549 GLU cc_start: 0.8720 (pm20) cc_final: 0.8347 (pm20) REVERT: B 667 GLU cc_start: 0.8923 (tp30) cc_final: 0.8570 (tp30) REVERT: B 670 ASP cc_start: 0.9221 (m-30) cc_final: 0.9007 (m-30) REVERT: B 820 MET cc_start: 0.8706 (mmm) cc_final: 0.8333 (mmt) REVERT: B 867 LEU cc_start: 0.7752 (tt) cc_final: 0.7454 (mm) outliers start: 19 outliers final: 12 residues processed: 155 average time/residue: 0.2513 time to fit residues: 57.9817 Evaluate side-chains 145 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 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 B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 254 MET 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 85 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 119 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.087191 restraints weight = 20087.789| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.26 r_work: 0.2892 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14058 Z= 0.111 Angle : 0.510 12.218 19149 Z= 0.254 Chirality : 0.040 0.184 2272 Planarity : 0.004 0.054 2439 Dihedral : 3.788 14.292 1900 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.16 % Allowed : 13.00 % Favored : 85.84 % 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: 1.30 (0.20), residues: 1790 helix: 2.13 (0.18), residues: 898 sheet: -0.30 (0.33), residues: 199 loop : -0.43 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.005 0.001 HIS B 357 PHE 0.010 0.001 PHE A 779 TYR 0.021 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 734) hydrogen bonds : angle 4.09608 ( 2229) covalent geometry : bond 0.00262 (14058) covalent geometry : angle 0.50999 (19149) *********************** 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 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8374 (mtp) cc_final: 0.7937 (mtp) REVERT: A 845 MET cc_start: 0.8421 (mmm) cc_final: 0.8221 (mmm) REVERT: B 62 GLU cc_start: 0.8460 (mp0) cc_final: 0.7920 (pm20) REVERT: B 98 ARG cc_start: 0.8084 (ptt180) cc_final: 0.7642 (ptm160) REVERT: B 394 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7591 (ttpp) REVERT: B 427 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8393 (tm-30) REVERT: B 483 HIS cc_start: 0.8377 (t-170) cc_final: 0.8120 (t-170) REVERT: B 549 GLU cc_start: 0.8712 (pm20) cc_final: 0.8375 (pm20) REVERT: B 667 GLU cc_start: 0.8918 (tp30) cc_final: 0.8616 (tp30) REVERT: B 670 ASP cc_start: 0.9221 (m-30) cc_final: 0.9006 (m-30) REVERT: B 820 MET cc_start: 0.8711 (mmm) cc_final: 0.8339 (mmt) REVERT: B 867 LEU cc_start: 0.7712 (tt) cc_final: 0.7418 (mm) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.2648 time to fit residues: 59.2017 Evaluate side-chains 141 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 713 VAL 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 95 VAL Chi-restraints excluded: chain B residue 254 MET 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 46 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 145 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.087322 restraints weight = 20251.449| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.28 r_work: 0.2888 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14058 Z= 0.116 Angle : 0.513 12.011 19149 Z= 0.255 Chirality : 0.040 0.179 2272 Planarity : 0.004 0.056 2439 Dihedral : 3.795 14.289 1900 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.82 % Allowed : 13.48 % 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: 1.32 (0.20), residues: 1790 helix: 2.16 (0.18), residues: 896 sheet: -0.31 (0.33), residues: 199 loop : -0.44 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS B 357 PHE 0.010 0.001 PHE A 779 TYR 0.014 0.001 TYR A 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 734) hydrogen bonds : angle 4.09913 ( 2229) covalent geometry : bond 0.00276 (14058) covalent geometry : angle 0.51302 (19149) ********************** 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 142 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8357 (mtp) cc_final: 0.7921 (mtp) REVERT: B 62 GLU cc_start: 0.8465 (mp0) cc_final: 0.7915 (pm20) REVERT: B 98 ARG cc_start: 0.8090 (ptt180) cc_final: 0.7645 (ptm160) REVERT: B 394 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7562 (ttpp) REVERT: B 427 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8386 (tm-30) REVERT: B 483 HIS cc_start: 0.8352 (t-170) cc_final: 0.8102 (t-170) REVERT: B 549 GLU cc_start: 0.8705 (pm20) cc_final: 0.8358 (pm20) REVERT: B 667 GLU cc_start: 0.8925 (tp30) cc_final: 0.8623 (tp30) REVERT: B 670 ASP cc_start: 0.9231 (m-30) cc_final: 0.9019 (m-30) REVERT: B 820 MET cc_start: 0.8720 (mmm) cc_final: 0.8355 (mmt) REVERT: B 867 LEU cc_start: 0.7682 (tt) cc_final: 0.7394 (mm) outliers start: 12 outliers final: 12 residues processed: 138 average time/residue: 0.3122 time to fit residues: 63.1350 Evaluate side-chains 143 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 713 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 254 MET 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 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.086849 restraints weight = 20323.573| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.27 r_work: 0.2886 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14058 Z= 0.119 Angle : 0.516 11.818 19149 Z= 0.257 Chirality : 0.040 0.178 2272 Planarity : 0.004 0.057 2439 Dihedral : 3.809 14.369 1900 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 1.02 % Allowed : 13.34 % Favored : 85.64 % 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: 1.33 (0.20), residues: 1790 helix: 2.13 (0.18), residues: 899 sheet: -0.34 (0.33), residues: 200 loop : -0.37 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE A 779 TYR 0.018 0.001 TYR A 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 734) hydrogen bonds : angle 4.10328 ( 2229) covalent geometry : bond 0.00284 (14058) covalent geometry : angle 0.51593 (19149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7795.03 seconds wall clock time: 136 minutes 57.20 seconds (8217.20 seconds total)