Starting phenix.real_space_refine on Wed Mar 4 15:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ma8_63749/03_2026/9ma8_63749.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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 P 4 5.49 5 S 78 5.16 5 C 8960 2.51 5 N 2338 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14025 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'GLC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'GLC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G1P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.23 Number of scatterers: 14025 At special positions: 0 Unit cell: (100.43, 159.36, 131.97, 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 78 16.00 P 4 15.00 O 2645 8.00 N 2338 7.00 C 8960 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 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " " GLC B 2 " - " GLC B 3 " " GLC C 1 " - " GLC C 2 " " GLC C 2 " - " GLC C 3 " " GLC C 3 " - " GLC C 4 " " GLC C 4 " - " GLC C 5 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 452.8 milliseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 15 sheets defined 49.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.860A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.855A pdb=" N TRP A 40 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.665A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 128 through 144 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.975A pdb=" N THR A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 removed outlier: 3.527A pdb=" N LEU A 250 " --> pdb=" O TRP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.626A pdb=" N LEU A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 4.086A pdb=" N LEU A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.836A pdb=" N GLY A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 432 through 436 removed outlier: 4.348A pdb=" N MET A 436 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.506A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 548 through 563 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.625A pdb=" N SER A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 607 through 613 removed outlier: 4.617A pdb=" N GLU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 613 " --> pdb=" O LLP A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 613' Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 645 through 664 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 678 through 692 removed outlier: 4.162A pdb=" N VAL A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 696 Processing helix chain 'A' and resid 697 through 709 Processing helix chain 'A' and resid 710 through 741 removed outlier: 5.943A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.711A pdb=" N ASP A 844 " --> pdb=" O HIS A 841 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 845 " --> pdb=" O ARG A 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 841 through 845' Processing helix chain 'E' and resid 26 through 35 removed outlier: 4.018A pdb=" N ASP E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.640A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'E' and resid 82 through 101 removed outlier: 4.108A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 235 through 239 removed outlier: 4.084A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 267 Processing helix chain 'E' and resid 282 through 296 removed outlier: 4.054A pdb=" N LEU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 310 Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 337 through 343 removed outlier: 4.090A pdb=" N ARG E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 354 Processing helix chain 'E' and resid 365 through 374 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 393 through 397 removed outlier: 3.811A pdb=" N LYS E 397 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 432 through 439 removed outlier: 4.228A pdb=" N MET E 436 " --> pdb=" O LYS E 433 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN E 439 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 4.099A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 452 through 482 removed outlier: 3.533A pdb=" N ILE E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 488 through 496 removed outlier: 3.848A pdb=" N ILE E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 520 removed outlier: 3.648A pdb=" N THR E 520 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 549 through 563 Processing helix chain 'E' and resid 578 through 589 Processing helix chain 'E' and resid 605 through 611 removed outlier: 3.517A pdb=" N ALA E 610 " --> pdb=" O SER E 606 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 611 " --> pdb=" O GLY E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 629 Processing helix chain 'E' and resid 645 through 664 Processing helix chain 'E' and resid 664 through 670 removed outlier: 3.554A pdb=" N MET E 668 " --> pdb=" O ASP E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 692 Processing helix chain 'E' and resid 693 through 696 Processing helix chain 'E' and resid 697 through 709 removed outlier: 3.818A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 741 removed outlier: 6.320A pdb=" N ASN E 723 " --> pdb=" O LYS E 719 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP E 724 " --> pdb=" O LEU E 720 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 727 " --> pdb=" O ASN E 723 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA E 728 " --> pdb=" O ASP E 724 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.496A pdb=" N ALA A 111 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR A 274 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR A 314 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS A 276 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 376 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 153 removed outlier: 6.377A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 153 removed outlier: 6.377A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 573 removed outlier: 6.899A pdb=" N LEU A 501 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE A 539 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 503 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER A 541 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 505 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP A 592 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 746 through 751 removed outlier: 3.818A pdb=" N VAL A 748 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS A 750 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A 767 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 768 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 811 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY A 806 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU A 815 " --> pdb=" O MET A 804 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N MET A 804 " --> pdb=" O GLU A 815 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 758 through 759 removed outlier: 6.798A pdb=" N ALA A 758 " --> pdb=" O LYS E 19 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N SER A 825 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU A 788 " --> pdb=" O SER A 825 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 782 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS A 787 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 796 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN A 789 " --> pdb=" O LYS A 794 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS A 794 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 149 through 153 removed outlier: 6.012A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 222 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 149 through 153 removed outlier: 6.012A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 222 " --> pdb=" O TRP E 211 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR E 201 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 162 through 164 Processing sheet with id=AB3, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.689A pdb=" N TYR E 313 " --> pdb=" O ASN E 378 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 571 through 573 removed outlier: 8.453A pdb=" N ILE E 572 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE E 538 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 501 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE E 539 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 503 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TRP E 592 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL E 620 " --> pdb=" O TRP E 592 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN E 594 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 746 through 747 removed outlier: 4.038A pdb=" N HIS E 746 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY E 806 " --> pdb=" O THR E 813 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU E 815 " --> pdb=" O MET E 804 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N MET E 804 " --> pdb=" O GLU E 815 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 794 through 801 removed outlier: 8.519A pdb=" N VAL E 796 " --> pdb=" O GLN E 789 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N GLN E 789 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ALA E 798 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS E 787 " --> pdb=" O ALA E 798 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR E 800 " --> pdb=" O VAL E 785 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL E 785 " --> pdb=" O TYR E 800 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL E 830 " --> pdb=" O LEU E 851 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2383 1.32 - 1.44: 4016 1.44 - 1.57: 7850 1.57 - 1.69: 3 1.69 - 1.81: 130 Bond restraints: 14382 Sorted by residual: bond pdb=" O1 G1P A 901 " pdb=" P G1P A 901 " ideal model delta sigma weight residual 1.743 1.601 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.613 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.614 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N VAL E 206 " pdb=" CA VAL E 206 " ideal model delta sigma weight residual 1.458 1.499 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" C5' LLP E 609 " pdb=" OP4 LLP E 609 " ideal model delta sigma weight residual 1.396 1.462 -0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 14377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18570 2.09 - 4.18: 802 4.18 - 6.28: 90 6.28 - 8.37: 11 8.37 - 10.46: 3 Bond angle restraints: 19476 Sorted by residual: angle pdb=" C PRO E 200 " pdb=" CA PRO E 200 " pdb=" CB PRO E 200 " ideal model delta sigma weight residual 112.27 101.81 10.46 1.56e+00 4.11e-01 4.50e+01 angle pdb=" C THR E 202 " pdb=" CA THR E 202 " pdb=" CB THR E 202 " ideal model delta sigma weight residual 117.23 110.05 7.18 1.36e+00 5.41e-01 2.79e+01 angle pdb=" N LYS A 513 " pdb=" CA LYS A 513 " pdb=" C LYS A 513 " ideal model delta sigma weight residual 113.16 106.96 6.20 1.24e+00 6.50e-01 2.50e+01 angle pdb=" CA GLY A 158 " pdb=" C GLY A 158 " pdb=" O GLY A 158 " ideal model delta sigma weight residual 122.56 117.77 4.79 1.03e+00 9.43e-01 2.16e+01 angle pdb=" CA LYS E 24 " pdb=" C LYS E 24 " pdb=" O LYS E 24 " ideal model delta sigma weight residual 121.55 116.64 4.91 1.06e+00 8.90e-01 2.15e+01 ... (remaining 19471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7261 17.77 - 35.55: 1006 35.55 - 53.32: 270 53.32 - 71.10: 66 71.10 - 88.87: 22 Dihedral angle restraints: 8625 sinusoidal: 3643 harmonic: 4982 Sorted by residual: dihedral pdb=" CA PHE A 709 " pdb=" C PHE A 709 " pdb=" N TYR A 710 " pdb=" CA TYR A 710 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ARG E 598 " pdb=" C ARG E 598 " pdb=" N PRO E 599 " pdb=" CA PRO E 599 " ideal model delta harmonic sigma weight residual 0.00 -20.79 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE E 331 " pdb=" C PHE E 331 " pdb=" N GLY E 332 " pdb=" CA GLY E 332 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1974 0.133 - 0.266: 63 0.266 - 0.399: 2 0.399 - 0.532: 0 0.532 - 0.665: 2 Chirality restraints: 2041 Sorted by residual: chirality pdb=" C1 GLC B 3 " pdb=" O4 GLC B 2 " pdb=" C2 GLC B 3 " pdb=" O5 GLC B 3 " both_signs ideal model delta sigma weight residual False 2.40 1.73 0.67 2.00e-02 2.50e+03 1.11e+03 chirality pdb=" C1 GLC C 5 " pdb=" O4 GLC C 4 " pdb=" C2 GLC C 5 " pdb=" O5 GLC C 5 " both_signs ideal model delta sigma weight residual False 2.40 1.83 0.57 2.00e-02 2.50e+03 8.24e+02 chirality pdb=" C1 GLC C 3 " pdb=" O4 GLC C 2 " pdb=" C2 GLC C 3 " pdb=" O5 GLC C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.22 0.18 2.00e-02 2.50e+03 8.43e+01 ... (remaining 2038 not shown) Planarity restraints: 2498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 21 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C SER E 21 " 0.068 2.00e-02 2.50e+03 pdb=" O SER E 21 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU E 22 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 238 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C THR E 238 " 0.060 2.00e-02 2.50e+03 pdb=" O THR E 238 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 239 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 609 " -0.027 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" NZ LLP A 609 " 0.024 2.00e-02 2.50e+03 pdb=" C4 LLP A 609 " -0.029 2.00e-02 2.50e+03 pdb=" C4' LLP A 609 " 0.032 2.00e-02 2.50e+03 ... (remaining 2495 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1411 2.74 - 3.28: 14439 3.28 - 3.82: 23967 3.82 - 4.36: 27643 4.36 - 4.90: 46948 Nonbonded interactions: 114408 Sorted by model distance: nonbonded pdb=" OH TYR E 201 " pdb=" O LYS E 251 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 165 " pdb=" OD1 ASP A 167 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN E 285 " pdb=" NH1 ARG E 288 " model vdw 2.212 3.120 nonbonded pdb=" OE2 GLU A 247 " pdb=" OH TYR A 334 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN E 178 " pdb=" OG SER E 181 " model vdw 2.223 3.040 ... (remaining 114403 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 1 through 852) selection = (chain 'E' and resid 1 through 852) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.420 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 14388 Z= 0.418 Angle : 0.892 10.462 19494 Z= 0.569 Chirality : 0.060 0.665 2041 Planarity : 0.004 0.059 2498 Dihedral : 17.930 88.873 5445 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.50 % Favored : 91.38 % Rotamer: Outliers : 3.80 % Allowed : 25.10 % Favored : 71.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1694 helix: 0.59 (0.20), residues: 728 sheet: -1.12 (0.32), residues: 260 loop : -1.82 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 354 TYR 0.032 0.001 TYR E 155 PHE 0.027 0.002 PHE A 331 TRP 0.025 0.002 TRP E 246 HIS 0.005 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00690 (14382) covalent geometry : angle 0.88860 (19476) hydrogen bonds : bond 0.18588 ( 593) hydrogen bonds : angle 7.31456 ( 1683) link_ALPHA1-4 : bond 0.00219 ( 6) link_ALPHA1-4 : angle 2.81941 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7222 (t70) cc_final: 0.6491 (p0) REVERT: A 99 MET cc_start: 0.9125 (tpp) cc_final: 0.8598 (tpt) REVERT: A 132 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8882 (tpp) REVERT: A 159 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.7940 (t80) REVERT: A 239 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: A 352 MET cc_start: 0.8075 (ttm) cc_final: 0.7808 (ttm) REVERT: A 548 ASP cc_start: 0.6944 (t0) cc_final: 0.6737 (t0) REVERT: A 852 ASN cc_start: 0.7155 (m110) cc_final: 0.6281 (t0) REVERT: E 178 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8370 (p0) REVERT: E 403 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7490 (mt-10) outliers start: 56 outliers final: 38 residues processed: 178 average time/residue: 0.1046 time to fit residues: 28.6683 Evaluate side-chains 151 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 CYS Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 509 PHE Chi-restraints excluded: chain E residue 725 ASN Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 828 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 178 ASN E 277 ASN E 361 ASN E 482 ASN E 711 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066011 restraints weight = 43450.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.067787 restraints weight = 25490.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069000 restraints weight = 17804.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.069810 restraints weight = 13903.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070339 restraints weight = 11669.745| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14388 Z= 0.134 Angle : 0.567 8.432 19494 Z= 0.295 Chirality : 0.041 0.158 2041 Planarity : 0.004 0.060 2498 Dihedral : 7.942 84.088 2153 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.32 % Allowed : 25.44 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1694 helix: 1.05 (0.19), residues: 726 sheet: -0.95 (0.32), residues: 266 loop : -1.66 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.018 0.001 TYR E 577 PHE 0.023 0.001 PHE E 709 TRP 0.011 0.001 TRP E 346 HIS 0.003 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00288 (14382) covalent geometry : angle 0.56511 (19476) hydrogen bonds : bond 0.04920 ( 593) hydrogen bonds : angle 5.34753 ( 1683) link_ALPHA1-4 : bond 0.00914 ( 6) link_ALPHA1-4 : angle 1.69340 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.9110 (tpp) cc_final: 0.8753 (tpt) REVERT: A 159 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 239 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 277 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: A 852 ASN cc_start: 0.7156 (m110) cc_final: 0.6286 (t0) REVERT: E 253 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: E 403 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: E 756 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6749 (mtt) REVERT: E 845 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7396 (t80) outliers start: 49 outliers final: 26 residues processed: 161 average time/residue: 0.0991 time to fit residues: 25.1920 Evaluate side-chains 140 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 593 MET Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 845 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3230 r_free = 0.3230 target = 0.077398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.065076 restraints weight = 43711.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066838 restraints weight = 25846.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.068055 restraints weight = 18164.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068858 restraints weight = 14179.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.069427 restraints weight = 11962.180| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14388 Z= 0.132 Angle : 0.535 7.400 19494 Z= 0.274 Chirality : 0.040 0.154 2041 Planarity : 0.004 0.058 2498 Dihedral : 7.161 86.410 2118 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.80 % Allowed : 25.03 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1694 helix: 1.44 (0.19), residues: 716 sheet: -0.90 (0.32), residues: 278 loop : -1.53 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.015 0.001 TYR E 155 PHE 0.015 0.001 PHE E 349 TRP 0.008 0.001 TRP E 211 HIS 0.009 0.001 HIS E 841 Details of bonding type rmsd covalent geometry : bond 0.00289 (14382) covalent geometry : angle 0.53335 (19476) hydrogen bonds : bond 0.04234 ( 593) hydrogen bonds : angle 4.96420 ( 1683) link_ALPHA1-4 : bond 0.00689 ( 6) link_ALPHA1-4 : angle 1.52149 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.9127 (tpp) cc_final: 0.8740 (tpt) REVERT: A 159 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8106 (t80) REVERT: A 160 PHE cc_start: 0.9159 (p90) cc_final: 0.8895 (p90) REVERT: A 239 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: E 403 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: E 686 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8303 (mmtt) REVERT: E 756 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6780 (mtt) REVERT: E 831 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6528 (ptp-170) REVERT: E 845 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7474 (t80) outliers start: 56 outliers final: 33 residues processed: 157 average time/residue: 0.0996 time to fit residues: 25.2505 Evaluate side-chains 138 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 819 GLU Chi-restraints excluded: chain E residue 831 ARG Chi-restraints excluded: chain E residue 845 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 121 GLN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 277 ASN ** E 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.071688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059471 restraints weight = 44700.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.061045 restraints weight = 26855.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.062146 restraints weight = 19241.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062894 restraints weight = 15261.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.063336 restraints weight = 12987.183| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 14388 Z= 0.363 Angle : 0.744 8.032 19494 Z= 0.385 Chirality : 0.047 0.168 2041 Planarity : 0.005 0.063 2498 Dihedral : 7.680 80.935 2113 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.56 % Allowed : 24.15 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1694 helix: 0.91 (0.19), residues: 724 sheet: -1.08 (0.32), residues: 278 loop : -1.59 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 514 TYR 0.022 0.002 TYR E 705 PHE 0.020 0.002 PHE E 812 TRP 0.019 0.002 TRP E 850 HIS 0.006 0.002 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00826 (14382) covalent geometry : angle 0.74075 (19476) hydrogen bonds : bond 0.05403 ( 593) hydrogen bonds : angle 5.34867 ( 1683) link_ALPHA1-4 : bond 0.00691 ( 6) link_ALPHA1-4 : angle 2.33060 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 102 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 7 TYR cc_start: 0.6516 (t80) cc_final: 0.5452 (p90) REVERT: A 159 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.7984 (t80) REVERT: A 239 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: A 374 CYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 253 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7024 (mm-30) REVERT: E 403 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: E 756 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7002 (mtt) REVERT: E 831 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7040 (ptp-170) outliers start: 82 outliers final: 56 residues processed: 175 average time/residue: 0.0956 time to fit residues: 27.0959 Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 92 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 509 PHE Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 657 ILE Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 828 THR Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063619 restraints weight = 42852.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.065338 restraints weight = 25128.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066544 restraints weight = 17683.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067358 restraints weight = 13820.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067876 restraints weight = 11620.015| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14388 Z= 0.128 Angle : 0.564 8.148 19494 Z= 0.287 Chirality : 0.041 0.155 2041 Planarity : 0.004 0.057 2498 Dihedral : 7.130 78.410 2111 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.80 % Allowed : 25.85 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1694 helix: 1.33 (0.19), residues: 716 sheet: -0.88 (0.32), residues: 286 loop : -1.51 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.017 0.001 TYR E 112 PHE 0.015 0.001 PHE E 349 TRP 0.010 0.001 TRP A 211 HIS 0.005 0.001 HIS E 841 Details of bonding type rmsd covalent geometry : bond 0.00279 (14382) covalent geometry : angle 0.56272 (19476) hydrogen bonds : bond 0.04265 ( 593) hydrogen bonds : angle 4.85653 ( 1683) link_ALPHA1-4 : bond 0.00810 ( 6) link_ALPHA1-4 : angle 1.52957 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 0.442 Fit side-chains REVERT: A 7 TYR cc_start: 0.6555 (t80) cc_final: 0.5362 (p90) REVERT: A 36 MET cc_start: 0.9152 (mmm) cc_final: 0.8918 (tpp) REVERT: A 159 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 239 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: A 492 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8941 (mp) REVERT: A 612 MET cc_start: 0.8937 (mmm) cc_final: 0.8352 (mmm) REVERT: A 698 MET cc_start: 0.8842 (ttm) cc_final: 0.8567 (ttm) REVERT: E 403 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: E 756 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6935 (mtt) REVERT: E 831 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6832 (ptp-170) REVERT: E 845 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7519 (t80) outliers start: 56 outliers final: 34 residues processed: 147 average time/residue: 0.0938 time to fit residues: 22.2596 Evaluate side-chains 133 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 831 ARG Chi-restraints excluded: chain E residue 845 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 ASN ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062608 restraints weight = 43129.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.064394 restraints weight = 25009.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.065595 restraints weight = 17405.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.066410 restraints weight = 13618.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066966 restraints weight = 11460.593| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14388 Z= 0.168 Angle : 0.569 10.084 19494 Z= 0.286 Chirality : 0.041 0.161 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.975 73.099 2111 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.27 % Allowed : 25.37 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1694 helix: 1.42 (0.19), residues: 708 sheet: -0.78 (0.32), residues: 286 loop : -1.37 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.014 0.001 TYR E 155 PHE 0.011 0.001 PHE E 331 TRP 0.009 0.001 TRP E 457 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00382 (14382) covalent geometry : angle 0.56692 (19476) hydrogen bonds : bond 0.04215 ( 593) hydrogen bonds : angle 4.81058 ( 1683) link_ALPHA1-4 : bond 0.00726 ( 6) link_ALPHA1-4 : angle 1.76563 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 0.537 Fit side-chains REVERT: A 7 TYR cc_start: 0.6601 (t80) cc_final: 0.5389 (p90) REVERT: A 159 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 239 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 335 MET cc_start: 0.7638 (tpt) cc_final: 0.7316 (tpt) REVERT: A 492 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8946 (mp) REVERT: A 612 MET cc_start: 0.9041 (mmm) cc_final: 0.8366 (mmm) REVERT: E 403 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: E 756 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: E 831 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6323 (ptp90) outliers start: 63 outliers final: 50 residues processed: 149 average time/residue: 0.0931 time to fit residues: 22.4536 Evaluate side-chains 149 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 93 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3200 r_free = 0.3200 target = 0.075601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063463 restraints weight = 42940.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065187 restraints weight = 25195.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.066338 restraints weight = 17571.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.067110 restraints weight = 13773.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.067656 restraints weight = 11631.759| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14388 Z= 0.147 Angle : 0.559 11.321 19494 Z= 0.279 Chirality : 0.041 0.153 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.797 72.146 2111 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.34 % Allowed : 24.97 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1694 helix: 1.37 (0.20), residues: 720 sheet: -0.53 (0.33), residues: 276 loop : -1.33 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.016 0.001 TYR A 577 PHE 0.009 0.001 PHE E 331 TRP 0.008 0.001 TRP E 457 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00333 (14382) covalent geometry : angle 0.55692 (19476) hydrogen bonds : bond 0.04021 ( 593) hydrogen bonds : angle 4.71229 ( 1683) link_ALPHA1-4 : bond 0.00817 ( 6) link_ALPHA1-4 : angle 1.70581 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 97 time to evaluate : 0.519 Fit side-chains REVERT: A 7 TYR cc_start: 0.6445 (t80) cc_final: 0.5438 (p90) REVERT: A 124 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8177 (ttmm) REVERT: A 159 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 239 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: A 247 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: A 492 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 612 MET cc_start: 0.8990 (mmm) cc_final: 0.8322 (mmm) REVERT: A 698 MET cc_start: 0.8901 (ttm) cc_final: 0.8647 (ttm) REVERT: E 403 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: E 756 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6956 (mtt) outliers start: 64 outliers final: 47 residues processed: 153 average time/residue: 0.0957 time to fit residues: 23.6241 Evaluate side-chains 147 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 93 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 509 PHE Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3218 r_free = 0.3218 target = 0.076469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064361 restraints weight = 42700.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.066102 restraints weight = 24970.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.067264 restraints weight = 17405.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068058 restraints weight = 13608.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.068451 restraints weight = 11449.218| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14388 Z= 0.124 Angle : 0.544 11.765 19494 Z= 0.272 Chirality : 0.040 0.153 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.564 74.134 2111 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.73 % Allowed : 26.19 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1694 helix: 1.64 (0.20), residues: 696 sheet: -0.57 (0.32), residues: 286 loop : -1.33 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.018 0.001 TYR E 155 PHE 0.009 0.001 PHE E 95 TRP 0.008 0.001 TRP E 386 HIS 0.004 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00278 (14382) covalent geometry : angle 0.54245 (19476) hydrogen bonds : bond 0.03828 ( 593) hydrogen bonds : angle 4.61751 ( 1683) link_ALPHA1-4 : bond 0.00685 ( 6) link_ALPHA1-4 : angle 1.61069 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 99 time to evaluate : 0.540 Fit side-chains REVERT: A 124 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8212 (ttmm) REVERT: A 159 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 239 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: A 247 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: A 331 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 492 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8925 (mp) REVERT: A 597 THR cc_start: 0.8837 (m) cc_final: 0.8567 (t) REVERT: A 612 MET cc_start: 0.8977 (mmm) cc_final: 0.8253 (mmm) REVERT: A 698 MET cc_start: 0.8910 (ttm) cc_final: 0.8598 (ttm) REVERT: E 756 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.6915 (mtt) outliers start: 55 outliers final: 43 residues processed: 146 average time/residue: 0.0960 time to fit residues: 22.7935 Evaluate side-chains 144 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 461 MET Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 159 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3222 r_free = 0.3222 target = 0.076701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.064537 restraints weight = 42795.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066282 restraints weight = 25164.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067438 restraints weight = 17553.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.068227 restraints weight = 13738.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068767 restraints weight = 11574.424| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14388 Z= 0.115 Angle : 0.545 12.303 19494 Z= 0.270 Chirality : 0.040 0.168 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.397 71.779 2108 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.60 % Allowed : 26.73 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1694 helix: 1.49 (0.20), residues: 722 sheet: -0.33 (0.32), residues: 276 loop : -1.45 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.028 0.001 TYR E 155 PHE 0.009 0.001 PHE E 95 TRP 0.051 0.001 TRP A 13 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00258 (14382) covalent geometry : angle 0.54307 (19476) hydrogen bonds : bond 0.03735 ( 593) hydrogen bonds : angle 4.55278 ( 1683) link_ALPHA1-4 : bond 0.00700 ( 6) link_ALPHA1-4 : angle 1.56903 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.542 Fit side-chains REVERT: A 124 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8114 (ttmm) REVERT: A 159 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.7964 (t80) REVERT: A 166 MET cc_start: 0.7972 (tpp) cc_final: 0.7716 (mtm) REVERT: A 239 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: A 247 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: A 331 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7803 (t80) REVERT: A 335 MET cc_start: 0.6949 (tpt) cc_final: 0.6502 (tpt) REVERT: A 492 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (mp) REVERT: A 597 THR cc_start: 0.8837 (m) cc_final: 0.8559 (t) REVERT: A 612 MET cc_start: 0.8984 (mmm) cc_final: 0.8271 (mmm) REVERT: A 698 MET cc_start: 0.8915 (ttm) cc_final: 0.8579 (ttm) REVERT: E 403 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: E 698 MET cc_start: 0.8133 (tpp) cc_final: 0.7922 (tpt) REVERT: E 756 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: E 845 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7727 (t80) outliers start: 53 outliers final: 43 residues processed: 143 average time/residue: 0.0895 time to fit residues: 20.9097 Evaluate side-chains 149 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 845 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 164 optimal weight: 0.0980 chunk 74 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3200 r_free = 0.3200 target = 0.075590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063120 restraints weight = 43358.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.064903 restraints weight = 25003.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.066110 restraints weight = 17343.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066919 restraints weight = 13487.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067430 restraints weight = 11327.025| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14388 Z= 0.159 Angle : 0.565 12.901 19494 Z= 0.282 Chirality : 0.041 0.168 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.459 72.850 2108 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.87 % Allowed : 26.53 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1694 helix: 1.60 (0.20), residues: 708 sheet: -0.38 (0.32), residues: 276 loop : -1.29 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.023 0.001 TYR E 155 PHE 0.009 0.001 PHE E 160 TRP 0.039 0.001 TRP A 13 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00361 (14382) covalent geometry : angle 0.56323 (19476) hydrogen bonds : bond 0.03912 ( 593) hydrogen bonds : angle 4.59663 ( 1683) link_ALPHA1-4 : bond 0.00708 ( 6) link_ALPHA1-4 : angle 1.72285 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 96 time to evaluate : 0.561 Fit side-chains REVERT: A 159 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.7966 (t80) REVERT: A 239 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: A 247 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: A 331 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 492 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 597 THR cc_start: 0.8868 (m) cc_final: 0.8609 (t) REVERT: A 612 MET cc_start: 0.9091 (mmm) cc_final: 0.8306 (mmm) REVERT: A 698 MET cc_start: 0.8996 (ttm) cc_final: 0.8665 (ttm) REVERT: E 403 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: E 756 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.6981 (mtt) REVERT: E 845 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7899 (t80) outliers start: 57 outliers final: 46 residues processed: 145 average time/residue: 0.0890 time to fit residues: 21.1366 Evaluate side-chains 149 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 7 TYR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 562 SER Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 756 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 765 LYS Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 845 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 GLN ** 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 = 0.3226 r_free = 0.3226 target = 0.076895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.064741 restraints weight = 42779.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.066476 restraints weight = 25194.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067640 restraints weight = 17638.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.068426 restraints weight = 13805.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068935 restraints weight = 11636.074| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14388 Z= 0.114 Angle : 0.546 12.768 19494 Z= 0.269 Chirality : 0.040 0.169 2041 Planarity : 0.004 0.058 2498 Dihedral : 6.448 86.941 2108 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.46 % Allowed : 27.20 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1694 helix: 1.52 (0.20), residues: 722 sheet: -0.30 (0.32), residues: 276 loop : -1.39 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.024 0.001 TYR E 155 PHE 0.009 0.001 PHE E 95 TRP 0.038 0.001 TRP A 13 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00254 (14382) covalent geometry : angle 0.54424 (19476) hydrogen bonds : bond 0.03659 ( 593) hydrogen bonds : angle 4.50320 ( 1683) link_ALPHA1-4 : bond 0.00700 ( 6) link_ALPHA1-4 : angle 1.55033 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.71 seconds wall clock time: 35 minutes 40.79 seconds (2140.79 seconds total)