Starting phenix.real_space_refine on Thu Jun 12 13:32:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy8_42795/06_2025/8uy8_42795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy8_42795/06_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_42795/06_2025/8uy8_42795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy8_42795/06_2025/8uy8_42795.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy8_42795/06_2025/8uy8_42795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy8_42795/06_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-5710/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: 9.08, per 1000 atoms: 0.65 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 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: 1.72 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: 5.62 Time building geometry restraints manager: 3.94 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: 3.870 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.110 Find NCS groups from input model: 0.640 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- 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 : 1.540 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: 0.3008 time to fit residues: 116.2376 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 : 1.550 ------------------------------------------------------------------------------- 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 = 0.113535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.085172 restraints weight = 20163.329| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.27 r_work: 0.2850 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14058 Z= 0.180 Angle : 0.576 8.749 19149 Z= 0.294 Chirality : 0.043 0.158 2272 Planarity : 0.005 0.054 2439 Dihedral : 4.251 29.677 1902 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % 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: 1.61 (0.18), residues: 906 sheet: -0.21 (0.35), residues: 172 loop : -0.64 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 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 0.04298 ( 734) hydrogen bonds : angle 4.63049 ( 2229) covalent geometry : bond 0.00437 (14058) covalent geometry : angle 0.57613 (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 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.683 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: 0.8138 (tttm) cc_final: 0.7370 (mttp) REVERT: A 226 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8141 (ptp90) REVERT: A 299 MET cc_start: 0.8469 (mtp) cc_final: 0.8036 (mtp) REVERT: A 620 MET cc_start: 0.8795 (mmp) cc_final: 0.7883 (tpt) REVERT: A 787 MET cc_start: 0.9072 (mmm) cc_final: 0.8808 (mmm) REVERT: B 98 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7666 (ptm160) REVERT: B 394 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7603 (ttpp) REVERT: B 549 GLU cc_start: 0.8565 (pm20) cc_final: 0.8311 (pm20) REVERT: B 820 MET cc_start: 0.8868 (mmt) cc_final: 0.8532 (mmm) REVERT: B 824 ARG cc_start: 0.8621 (tpp80) cc_final: 0.7694 (tpp-160) REVERT: B 867 LEU cc_start: 0.7831 (tt) cc_final: 0.7508 (mm) outliers start: 16 outliers final: 7 residues processed: 160 average time/residue: 0.4180 time to fit residues: 98.2810 Evaluate side-chains 136 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 741 GLN B 282 GLN B 863 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.085876 restraints weight = 20188.652| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.27 r_work: 0.2860 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14058 Z= 0.141 Angle : 0.518 6.810 19149 Z= 0.266 Chirality : 0.041 0.147 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.117 28.547 1902 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.02 % Allowed : 9.39 % Favored : 89.58 % 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: 1.78 (0.18), residues: 901 sheet: -0.33 (0.34), residues: 188 loop : -0.63 (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 0.019 0.001 PHE A 364 TYR 0.016 0.001 TYR B 698 ARG 0.005 0.000 ARG B 650 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 734) hydrogen bonds : angle 4.38443 ( 2229) covalent geometry : bond 0.00337 (14058) covalent geometry : angle 0.51778 (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 157 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 2.492 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8156 (tttm) cc_final: 0.7400 (mttp) REVERT: A 299 MET cc_start: 0.8407 (mtp) cc_final: 0.7942 (mtp) REVERT: A 359 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8987 (p0) REVERT: A 620 MET cc_start: 0.8804 (mmp) cc_final: 0.7859 (tpt) REVERT: A 728 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 787 MET cc_start: 0.9057 (mmm) cc_final: 0.8821 (mmm) REVERT: B 98 ARG cc_start: 0.8082 (ptt180) cc_final: 0.7684 (ptm160) REVERT: B 394 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7573 (ttpp) REVERT: B 549 GLU cc_start: 0.8622 (pm20) cc_final: 0.8329 (pm20) REVERT: B 867 LEU cc_start: 0.7848 (tt) cc_final: 0.7550 (mm) outliers start: 15 outliers final: 5 residues processed: 154 average time/residue: 0.4204 time to fit residues: 95.3887 Evaluate side-chains 136 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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: 0.1980 chunk 178 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.113943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.085681 restraints weight = 20147.270| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.27 r_work: 0.2864 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14058 Z= 0.142 Angle : 0.516 7.866 19149 Z= 0.263 Chirality : 0.041 0.147 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.021 18.245 1900 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.70 % Allowed : 10.14 % Favored : 88.16 % 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: 1.01 (0.20), residues: 1790 helix: 1.83 (0.18), residues: 898 sheet: -0.29 (0.34), residues: 194 loop : -0.55 (0.23), residues: 698 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 0.015 0.001 PHE A 364 TYR 0.016 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 734) hydrogen bonds : angle 4.29972 ( 2229) covalent geometry : bond 0.00345 (14058) covalent geometry : angle 0.51609 (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 161 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8116 (tttm) cc_final: 0.7340 (mttp) REVERT: A 359 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8992 (p0) REVERT: A 620 MET cc_start: 0.8803 (mmp) cc_final: 0.7840 (tpt) REVERT: B 62 GLU cc_start: 0.8410 (mp0) cc_final: 0.7820 (pm20) REVERT: B 98 ARG cc_start: 0.8094 (ptt180) cc_final: 0.7669 (ptm160) REVERT: B 394 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7545 (ttpp) REVERT: B 549 GLU cc_start: 0.8645 (pm20) cc_final: 0.8283 (pm20) REVERT: B 867 LEU cc_start: 0.7814 (tt) cc_final: 0.7515 (mm) outliers start: 25 outliers final: 11 residues processed: 157 average time/residue: 0.2693 time to fit residues: 64.1046 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 : 1.639 ------------------------------------------------------------------------------- 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 395 THR Chi-restraints excluded: chain A residue 713 VAL 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: 0.7980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 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 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 = 0.3411 r_free = 0.3411 target = 0.114252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086096 restraints weight = 20253.645| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.28 r_work: 0.2870 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14058 Z= 0.126 Angle : 0.502 8.095 19149 Z= 0.255 Chirality : 0.041 0.145 2272 Planarity : 0.004 0.052 2439 Dihedral : 3.945 17.385 1900 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.23 % Allowed : 10.69 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1790 helix: 1.91 (0.18), residues: 900 sheet: -0.28 (0.34), residues: 194 loop : -0.51 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.004 0.001 HIS B 357 PHE 0.013 0.001 PHE A 364 TYR 0.018 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 734) hydrogen bonds : angle 4.21730 ( 2229) covalent geometry : bond 0.00302 (14058) covalent geometry : angle 0.50164 (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 161 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8119 (tttm) cc_final: 0.7343 (mttp) REVERT: A 266 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: A 299 MET cc_start: 0.8400 (mtp) cc_final: 0.7983 (mtp) REVERT: A 359 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8978 (p0) REVERT: B 98 ARG cc_start: 0.8077 (ptt180) cc_final: 0.7643 (ptm160) REVERT: B 394 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7548 (ttpp) REVERT: B 427 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8422 (tm-30) REVERT: B 549 GLU cc_start: 0.8685 (pm20) cc_final: 0.8312 (pm20) REVERT: B 867 LEU cc_start: 0.7786 (tt) cc_final: 0.7497 (mm) outliers start: 18 outliers final: 14 residues processed: 158 average time/residue: 0.2614 time to fit residues: 60.5475 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 863 GLN Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 129 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 165 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.112848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084550 restraints weight = 20310.385| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.27 r_work: 0.2845 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14058 Z= 0.173 Angle : 0.536 9.252 19149 Z= 0.272 Chirality : 0.042 0.152 2272 Planarity : 0.005 0.051 2439 Dihedral : 4.026 16.702 1900 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 1.70 % Allowed : 10.82 % Favored : 87.47 % 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: 1.01 (0.20), residues: 1790 helix: 1.82 (0.18), residues: 900 sheet: -0.30 (0.33), residues: 194 loop : -0.52 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 263 HIS 0.008 0.001 HIS A 900 PHE 0.013 0.001 PHE A 779 TYR 0.022 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 734) hydrogen bonds : angle 4.27238 ( 2229) covalent geometry : bond 0.00424 (14058) covalent geometry : angle 0.53561 (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 162 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8141 (tttm) cc_final: 0.7354 (mttp) REVERT: A 299 MET cc_start: 0.8451 (mtp) cc_final: 0.8034 (mtp) REVERT: A 359 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.9010 (p0) REVERT: B 62 GLU cc_start: 0.8444 (mp0) cc_final: 0.7863 (pm20) REVERT: B 98 ARG cc_start: 0.8134 (ptt180) cc_final: 0.7690 (ptm160) REVERT: B 394 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7573 (ttpp) REVERT: B 427 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8428 (tm-30) REVERT: B 483 HIS cc_start: 0.8451 (t-170) cc_final: 0.8164 (t-170) REVERT: B 549 GLU cc_start: 0.8714 (pm20) cc_final: 0.8356 (pm20) REVERT: B 867 LEU cc_start: 0.7809 (tt) cc_final: 0.7509 (mm) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.2587 time to fit residues: 60.0498 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080960 restraints weight = 20504.992| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.26 r_work: 0.2787 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14058 Z= 0.284 Angle : 0.627 11.546 19149 Z= 0.318 Chirality : 0.046 0.193 2272 Planarity : 0.005 0.052 2439 Dihedral : 4.379 16.085 1900 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 1.63 % Allowed : 11.78 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1790 helix: 1.56 (0.18), residues: 888 sheet: -0.38 (0.34), residues: 192 loop : -0.63 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 263 HIS 0.005 0.001 HIS B 357 PHE 0.016 0.002 PHE A 802 TYR 0.029 0.002 TYR B 869 ARG 0.004 0.000 ARG B 343 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 734) hydrogen bonds : angle 4.52450 ( 2229) covalent geometry : bond 0.00701 (14058) covalent geometry : angle 0.62667 (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 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.501 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.8460 (mtp) cc_final: 0.8061 (mtp) REVERT: B 98 ARG cc_start: 0.8233 (ptt180) cc_final: 0.7749 (ptm160) REVERT: B 220 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 549 GLU cc_start: 0.8745 (pm20) cc_final: 0.8315 (pm20) REVERT: B 679 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8461 (mmp) REVERT: B 867 LEU cc_start: 0.7983 (tt) cc_final: 0.7686 (mm) outliers start: 24 outliers final: 19 residues processed: 149 average time/residue: 0.2601 time to fit residues: 57.4247 Evaluate side-chains 147 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 124 ILE 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 395 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 794 ASN 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 220 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 770 ILE 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: 0.8980 chunk 153 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085155 restraints weight = 20097.917| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.27 r_work: 0.2856 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14058 Z= 0.126 Angle : 0.519 9.344 19149 Z= 0.266 Chirality : 0.041 0.159 2272 Planarity : 0.005 0.054 2439 Dihedral : 4.110 15.901 1900 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 12.73 % Favored : 85.98 % 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: 0.96 (0.20), residues: 1790 helix: 1.79 (0.18), residues: 898 sheet: -0.40 (0.33), residues: 200 loop : -0.54 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 806 HIS 0.013 0.001 HIS A 900 PHE 0.012 0.001 PHE A 295 TYR 0.018 0.001 TYR B 869 ARG 0.003 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 734) hydrogen bonds : angle 4.28467 ( 2229) covalent geometry : bond 0.00299 (14058) covalent geometry : angle 0.51872 (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 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8147 (ptmm) REVERT: A 299 MET cc_start: 0.8396 (mtp) cc_final: 0.8008 (mtp) REVERT: B 62 GLU cc_start: 0.8493 (mp0) cc_final: 0.8201 (pm20) REVERT: B 98 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7681 (ptm160) REVERT: B 394 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7498 (ttpp) REVERT: B 549 GLU cc_start: 0.8703 (pm20) cc_final: 0.8308 (pm20) REVERT: B 867 LEU cc_start: 0.7875 (tt) cc_final: 0.7588 (mm) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.2824 time to fit residues: 61.8474 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 : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086362 restraints weight = 20073.424| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.26 r_work: 0.2870 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2302 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= 0.116 Angle : 0.507 7.451 19149 Z= 0.258 Chirality : 0.041 0.155 2272 Planarity : 0.005 0.055 2439 Dihedral : 3.969 20.578 1900 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 0.88 % Allowed : 13.34 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1790 helix: 1.93 (0.18), residues: 899 sheet: -0.35 (0.34), residues: 200 loop : -0.50 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.006 0.001 HIS B 357 PHE 0.011 0.001 PHE A 779 TYR 0.027 0.001 TYR B 869 ARG 0.004 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 734) hydrogen bonds : angle 4.18552 ( 2229) covalent geometry : bond 0.00273 (14058) covalent geometry : angle 0.50715 (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 149 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.929 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8206 (tttt) cc_final: 0.7418 (mttp) REVERT: A 299 MET cc_start: 0.8386 (mtp) cc_final: 0.7958 (mtp) REVERT: B 62 GLU cc_start: 0.8487 (mp0) cc_final: 0.7942 (pm20) REVERT: B 98 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7661 (ptm160) REVERT: B 394 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7521 (ttpp) REVERT: B 427 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8406 (tm-30) REVERT: B 549 GLU cc_start: 0.8721 (pm20) cc_final: 0.8353 (pm20) REVERT: B 867 LEU cc_start: 0.7803 (tt) cc_final: 0.7526 (mm) outliers start: 13 outliers final: 12 residues processed: 145 average time/residue: 0.3690 time to fit residues: 80.5832 Evaluate side-chains 144 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 46 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 900 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.085322 restraints weight = 20106.179| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.27 r_work: 0.2859 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14058 Z= 0.142 Angle : 0.522 7.927 19149 Z= 0.266 Chirality : 0.041 0.161 2272 Planarity : 0.005 0.054 2439 Dihedral : 3.996 15.657 1900 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.16 % Allowed : 13.41 % Favored : 85.43 % 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: 1.89 (0.18), residues: 899 sheet: -0.31 (0.34), residues: 199 loop : -0.50 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.006 0.001 HIS B 357 PHE 0.012 0.001 PHE A 779 TYR 0.025 0.001 TYR B 869 ARG 0.007 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 734) hydrogen bonds : angle 4.22131 ( 2229) covalent geometry : bond 0.00345 (14058) covalent geometry : angle 0.52174 (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 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8231 (tttt) cc_final: 0.7445 (mttp) REVERT: A 299 MET cc_start: 0.8397 (mtp) cc_final: 0.7958 (mtp) REVERT: B 62 GLU cc_start: 0.8491 (mp0) cc_final: 0.8216 (pm20) REVERT: B 98 ARG cc_start: 0.8102 (ptt180) cc_final: 0.7671 (ptm160) REVERT: B 394 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7551 (ttpp) REVERT: B 427 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8416 (tm-30) REVERT: B 549 GLU cc_start: 0.8712 (pm20) cc_final: 0.8350 (pm20) REVERT: B 667 GLU cc_start: 0.8918 (tp30) cc_final: 0.8565 (tp30) REVERT: B 867 LEU cc_start: 0.7849 (tt) cc_final: 0.7567 (mm) outliers start: 17 outliers final: 13 residues processed: 148 average time/residue: 0.2933 time to fit residues: 64.4707 Evaluate side-chains 144 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.086994 restraints weight = 20290.660| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.28 r_work: 0.2888 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14058 Z= 0.106 Angle : 0.504 8.589 19149 Z= 0.256 Chirality : 0.040 0.143 2272 Planarity : 0.005 0.060 2439 Dihedral : 3.890 14.198 1900 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 1.02 % Allowed : 13.89 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.20), residues: 1790 helix: 2.04 (0.18), residues: 899 sheet: -0.32 (0.34), residues: 199 loop : -0.46 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.012 0.001 HIS A 899 PHE 0.012 0.001 PHE A 779 TYR 0.012 0.001 TYR B 869 ARG 0.007 0.000 ARG B 529 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 734) hydrogen bonds : angle 4.13242 ( 2229) covalent geometry : bond 0.00243 (14058) covalent geometry : angle 0.50439 (19149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8787.27 seconds wall clock time: 155 minutes 7.59 seconds (9307.59 seconds total)