Starting phenix.real_space_refine on Wed Mar 12 04:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9n_27267/03_2025/8d9n_27267.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4840 2.51 5 N 1126 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7186 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3594 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3592 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Residues with excluded nonbonded symmetry interactions: 382 residue: pdb=" N SER A 420 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 420 " occ=0.00 residue: pdb=" N PRO A 421 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 421 " occ=0.00 residue: pdb=" N SER A 425 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 425 " occ=0.00 residue: pdb=" N ALA A 426 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 426 " occ=0.00 residue: pdb=" N PHE A 429 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 429 " occ=0.00 residue: pdb=" N TYR A 431 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 431 " occ=0.00 residue: pdb=" N PHE A 432 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 432 " occ=0.00 residue: pdb=" N ALA A 433 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 433 " occ=0.00 residue: pdb=" N ALA A 434 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 434 " occ=0.00 residue: pdb=" N PRO A 437 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 437 " occ=0.00 residue: pdb=" N ALA A 438 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 438 " occ=0.00 residue: pdb=" N PHE A 441 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 441 " occ=0.00 ... (remaining 370 not shown) Time building chain proxies: 4.65, per 1000 atoms: 0.65 Number of scatterers: 7186 At special positions: 0 Unit cell: (121.04, 77.52, 84.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1188 8.00 N 1126 7.00 C 4840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 966.3 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 70.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.795A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.875A pdb=" N THR A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.632A pdb=" N ALA A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.536A pdb=" N THR A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 525 removed outlier: 3.559A pdb=" N VAL A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 4.545A pdb=" N LEU A 530 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 534 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 565 removed outlier: 3.928A pdb=" N ILE A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 611 removed outlier: 3.513A pdb=" N THR A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 625 removed outlier: 3.631A pdb=" N ARG A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 632 through 642 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 686 through 703 removed outlier: 3.620A pdb=" N LEU A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 Processing helix chain 'A' and resid 776 through 791 removed outlier: 3.590A pdb=" N SER A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.664A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 832 removed outlier: 3.874A pdb=" N LEU A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 871 removed outlier: 3.688A pdb=" N HIS A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 853 " --> pdb=" O TRP A 849 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 854 " --> pdb=" O ARG A 850 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 removed outlier: 3.700A pdb=" N LEU A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.757A pdb=" N LEU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 897 removed outlier: 3.717A pdb=" N ILE A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'B' and resid 421 through 449 removed outlier: 3.795A pdb=" N ILE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Proline residue: B 437 - end of helix removed outlier: 3.875A pdb=" N THR B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.632A pdb=" N ALA B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 500 removed outlier: 3.536A pdb=" N THR B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 525 removed outlier: 3.559A pdb=" N VAL B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 removed outlier: 4.545A pdb=" N LEU B 530 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 534 " --> pdb=" O VAL B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 565 removed outlier: 3.928A pdb=" N ILE B 541 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 545 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 557 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.512A pdb=" N THR B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 600 " --> pdb=" O MET B 596 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 611 " --> pdb=" O ARG B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 625 removed outlier: 3.632A pdb=" N ARG B 620 " --> pdb=" O PRO B 616 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 632 through 642 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 686 through 703 removed outlier: 3.622A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 692 " --> pdb=" O PRO B 688 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 702 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 734 Processing helix chain 'B' and resid 776 through 791 removed outlier: 3.590A pdb=" N SER B 780 " --> pdb=" O GLU B 776 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.664A pdb=" N LEU B 806 " --> pdb=" O PRO B 802 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 818 " --> pdb=" O GLY B 814 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 820 " --> pdb=" O THR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 3.875A pdb=" N LEU B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 871 removed outlier: 3.689A pdb=" N HIS B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 853 " --> pdb=" O TRP B 849 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 854 " --> pdb=" O ARG B 850 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 861 " --> pdb=" O THR B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 884 removed outlier: 3.700A pdb=" N LEU B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.757A pdb=" N LEU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 897 removed outlier: 3.718A pdb=" N ILE B 896 " --> pdb=" O LEU B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481 Processing sheet with id=AA2, first strand: chain 'B' and resid 480 through 481 361 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2134 1.34 - 1.46: 1632 1.46 - 1.58: 3540 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7366 Sorted by residual: bond pdb=" N VAL B 784 " pdb=" CA VAL B 784 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.83e+00 bond pdb=" N ILE B 728 " pdb=" CA ILE B 728 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" N ILE A 549 " pdb=" CA ILE A 549 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.30e-02 5.92e+03 5.83e+00 bond pdb=" N HIS B 721 " pdb=" CA HIS B 721 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.38e+00 bond pdb=" N LEU A 545 " pdb=" CA LEU A 545 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.96e+00 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 9412 1.07 - 2.13: 452 2.13 - 3.20: 117 3.20 - 4.27: 39 4.27 - 5.33: 6 Bond angle restraints: 10026 Sorted by residual: angle pdb=" CA ILE B 728 " pdb=" C ILE B 728 " pdb=" O ILE B 728 " ideal model delta sigma weight residual 121.17 117.43 3.74 1.06e+00 8.90e-01 1.25e+01 angle pdb=" CA LEU B 515 " pdb=" C LEU B 515 " pdb=" O LEU B 515 " ideal model delta sigma weight residual 120.20 116.77 3.43 1.12e+00 7.97e-01 9.40e+00 angle pdb=" CA ILE A 549 " pdb=" C ILE A 549 " pdb=" O ILE A 549 " ideal model delta sigma weight residual 120.47 117.34 3.13 1.08e+00 8.57e-01 8.38e+00 angle pdb=" CA VAL B 784 " pdb=" C VAL B 784 " pdb=" O VAL B 784 " ideal model delta sigma weight residual 120.95 117.97 2.98 1.04e+00 9.25e-01 8.19e+00 angle pdb=" CA LEU A 545 " pdb=" C LEU A 545 " pdb=" O LEU A 545 " ideal model delta sigma weight residual 120.42 117.54 2.88 1.06e+00 8.90e-01 7.39e+00 ... (remaining 10021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 3926 16.05 - 32.09: 303 32.09 - 48.14: 76 48.14 - 64.19: 19 64.19 - 80.23: 8 Dihedral angle restraints: 4332 sinusoidal: 1718 harmonic: 2614 Sorted by residual: dihedral pdb=" CA MET A 635 " pdb=" C MET A 635 " pdb=" N VAL A 636 " pdb=" CA VAL A 636 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA MET B 635 " pdb=" C MET B 635 " pdb=" N VAL B 636 " pdb=" CA VAL B 636 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU B 590 " pdb=" C LEU B 590 " pdb=" N LEU B 591 " pdb=" CA LEU B 591 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 904 0.042 - 0.083: 240 0.083 - 0.125: 63 0.125 - 0.166: 8 0.166 - 0.208: 3 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA VAL B 747 " pdb=" N VAL B 747 " pdb=" C VAL B 747 " pdb=" CB VAL B 747 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 1215 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 680 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.47e+00 pdb=" CG TRP A 680 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 680 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 680 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 680 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 680 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 680 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 680 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 680 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 680 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 680 " -0.012 2.00e-02 2.50e+03 1.17e-02 3.43e+00 pdb=" CG TRP B 680 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 680 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 680 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 680 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 680 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 680 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 680 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 680 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 680 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 840 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 841 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 841 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 841 " 0.024 5.00e-02 4.00e+02 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 96 2.67 - 3.22: 7349 3.22 - 3.78: 10655 3.78 - 4.34: 14552 4.34 - 4.90: 22673 Nonbonded interactions: 55325 Sorted by model distance: nonbonded pdb=" O ILE B 696 " pdb=" OG SER B 700 " model vdw 2.107 3.040 nonbonded pdb=" O ILE A 696 " pdb=" OG SER A 700 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR A 431 " pdb=" OG SER A 791 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR B 431 " pdb=" OG SER B 791 " model vdw 2.168 3.040 nonbonded pdb=" O VAL B 479 " pdb=" OG1 THR B 745 " model vdw 2.183 3.040 ... (remaining 55320 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 420 through 706 or (resid 707 and (name N or name CA or na \ me C or name CB or name CG1 or name CG2 or name CD1)) or resid 720 through 746 o \ r (resid 747 and (name N or name CA or name C or name CB or name CG1 or name CG2 \ )) or resid 775 through 909)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.30 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: 0.310 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.070 Process input model: 19.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7366 Z= 0.178 Angle : 0.600 5.335 10026 Z= 0.336 Chirality : 0.042 0.208 1218 Planarity : 0.005 0.043 1208 Dihedral : 13.205 80.232 2640 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.38 % Allowed : 0.38 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.29), residues: 890 helix: 0.12 (0.24), residues: 508 sheet: None (None), residues: 0 loop : -1.38 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 680 HIS 0.001 0.000 HIS A 573 PHE 0.008 0.001 PHE B 513 TYR 0.006 0.001 TYR B 836 ARG 0.003 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: -0.0240 (t80) cc_final: -0.0486 (t80) REVERT: B 861 CYS cc_start: 0.3385 (m) cc_final: 0.2829 (p) outliers start: 3 outliers final: 0 residues processed: 94 average time/residue: 0.1394 time to fit residues: 19.5158 Evaluate side-chains 69 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.0020 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.245230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.216016 restraints weight = 39887.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.218445 restraints weight = 32848.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.220965 restraints weight = 27315.481| |-----------------------------------------------------------------------------| r_work (final): 0.5107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0507 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7366 Z= 0.174 Angle : 0.623 9.165 10026 Z= 0.307 Chirality : 0.043 0.167 1218 Planarity : 0.005 0.050 1208 Dihedral : 4.368 20.609 960 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 890 helix: 0.43 (0.23), residues: 560 sheet: None (None), residues: 0 loop : -1.27 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 866 HIS 0.003 0.001 HIS B 721 PHE 0.017 0.001 PHE A 489 TYR 0.011 0.001 TYR A 504 ARG 0.013 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 596 MET cc_start: 0.0095 (ptm) cc_final: -0.0295 (ptm) REVERT: A 739 MET cc_start: 0.4218 (mpp) cc_final: 0.3329 (mpp) REVERT: B 739 MET cc_start: 0.3967 (mpp) cc_final: 0.3027 (mpp) REVERT: B 861 CYS cc_start: 0.3978 (m) cc_final: 0.3709 (p) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1321 time to fit residues: 19.3647 Evaluate side-chains 62 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.245275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.216590 restraints weight = 41055.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.218619 restraints weight = 34956.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.221943 restraints weight = 30378.730| |-----------------------------------------------------------------------------| r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0438 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7366 Z= 0.154 Angle : 0.592 6.780 10026 Z= 0.288 Chirality : 0.043 0.173 1218 Planarity : 0.005 0.048 1208 Dihedral : 4.193 17.699 960 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 890 helix: 0.51 (0.23), residues: 554 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 866 HIS 0.002 0.001 HIS B 721 PHE 0.016 0.001 PHE B 807 TYR 0.006 0.001 TYR A 842 ARG 0.004 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 861 CYS cc_start: 0.3843 (m) cc_final: 0.3524 (p) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1308 time to fit residues: 18.0119 Evaluate side-chains 60 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5715 r_free = 0.5715 target = 0.247290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.222016 restraints weight = 41903.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.222795 restraints weight = 33931.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.222932 restraints weight = 26162.654| |-----------------------------------------------------------------------------| r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0537 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7366 Z= 0.142 Angle : 0.575 6.517 10026 Z= 0.274 Chirality : 0.042 0.165 1218 Planarity : 0.005 0.051 1208 Dihedral : 4.113 17.583 960 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.29), residues: 890 helix: 0.64 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 510 HIS 0.001 0.000 HIS A 852 PHE 0.017 0.001 PHE A 513 TYR 0.007 0.001 TYR A 842 ARG 0.004 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 861 CYS cc_start: 0.3465 (m) cc_final: 0.3130 (p) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1355 time to fit residues: 18.5047 Evaluate side-chains 58 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5706 r_free = 0.5706 target = 0.246012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.217395 restraints weight = 42030.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.218985 restraints weight = 37063.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.222643 restraints weight = 31480.846| |-----------------------------------------------------------------------------| r_work (final): 0.5161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0297 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7366 Z= 0.226 Angle : 0.623 6.191 10026 Z= 0.309 Chirality : 0.043 0.161 1218 Planarity : 0.005 0.046 1208 Dihedral : 4.134 18.349 960 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.30), residues: 890 helix: 0.75 (0.22), residues: 588 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 741 HIS 0.002 0.001 HIS A 721 PHE 0.019 0.001 PHE B 807 TYR 0.007 0.001 TYR A 842 ARG 0.001 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 861 CYS cc_start: 0.3953 (m) cc_final: 0.3512 (m) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1333 time to fit residues: 16.2295 Evaluate side-chains 56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN B 822 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5712 r_free = 0.5712 target = 0.246087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.221148 restraints weight = 42143.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.222248 restraints weight = 38130.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.222343 restraints weight = 25812.623| |-----------------------------------------------------------------------------| r_work (final): 0.5203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0147 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7366 Z= 0.210 Angle : 0.612 5.786 10026 Z= 0.301 Chirality : 0.043 0.189 1218 Planarity : 0.005 0.049 1208 Dihedral : 4.210 18.580 960 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.25 % Allowed : 2.63 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.30), residues: 890 helix: 0.88 (0.22), residues: 587 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 866 HIS 0.002 0.001 HIS B 852 PHE 0.017 0.001 PHE A 807 TYR 0.006 0.001 TYR A 646 ARG 0.002 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: -0.4991 (p0) cc_final: -0.6493 (t0) REVERT: A 739 MET cc_start: 0.4248 (mpp) cc_final: 0.3767 (mpp) REVERT: B 447 ASP cc_start: -0.5363 (p0) cc_final: -0.6548 (t0) REVERT: B 739 MET cc_start: 0.4034 (mpp) cc_final: 0.3513 (mpp) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.1362 time to fit residues: 16.3794 Evaluate side-chains 53 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 73 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5709 r_free = 0.5709 target = 0.246105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5290 r_free = 0.5290 target = 0.218980 restraints weight = 42238.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.219210 restraints weight = 39413.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.219383 restraints weight = 37478.091| |-----------------------------------------------------------------------------| r_work (final): 0.5145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0435 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7366 Z= 0.148 Angle : 0.613 6.411 10026 Z= 0.291 Chirality : 0.044 0.157 1218 Planarity : 0.005 0.047 1208 Dihedral : 4.175 19.144 960 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.30), residues: 890 helix: 0.91 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -1.32 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 866 HIS 0.006 0.001 HIS B 852 PHE 0.029 0.001 PHE B 489 TYR 0.005 0.001 TYR A 842 ARG 0.002 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 PHE cc_start: 0.0544 (t80) cc_final: -0.0267 (t80) REVERT: B 861 CYS cc_start: 0.3797 (m) cc_final: 0.3426 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1630 time to fit residues: 20.7321 Evaluate side-chains 57 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5714 r_free = 0.5714 target = 0.246963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5358 r_free = 0.5358 target = 0.222723 restraints weight = 43208.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.223494 restraints weight = 37293.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.223517 restraints weight = 27623.979| |-----------------------------------------------------------------------------| r_work (final): 0.5128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0449 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7366 Z= 0.192 Angle : 0.628 6.544 10026 Z= 0.302 Chirality : 0.043 0.154 1218 Planarity : 0.005 0.048 1208 Dihedral : 4.169 18.131 960 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 890 helix: 0.88 (0.22), residues: 581 sheet: None (None), residues: 0 loop : -1.28 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 866 HIS 0.006 0.001 HIS B 852 PHE 0.018 0.001 PHE A 489 TYR 0.007 0.001 TYR B 842 ARG 0.002 0.000 ARG A 869 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 693 PHE cc_start: -0.0083 (t80) cc_final: -0.0735 (t80) REVERT: B 861 CYS cc_start: 0.3891 (m) cc_final: 0.3472 (m) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1364 time to fit residues: 16.5508 Evaluate side-chains 54 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5710 r_free = 0.5710 target = 0.246267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.221801 restraints weight = 43440.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.222615 restraints weight = 35798.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.222615 restraints weight = 26997.448| |-----------------------------------------------------------------------------| r_work (final): 0.5349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0456 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7366 Z= 0.163 Angle : 0.619 6.297 10026 Z= 0.296 Chirality : 0.044 0.182 1218 Planarity : 0.005 0.047 1208 Dihedral : 4.209 18.588 960 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.30), residues: 890 helix: 1.00 (0.23), residues: 576 sheet: None (None), residues: 0 loop : -1.12 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 680 HIS 0.006 0.001 HIS B 852 PHE 0.017 0.001 PHE A 489 TYR 0.006 0.001 TYR B 842 ARG 0.002 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: -0.6466 (pp) cc_final: -0.6681 (pp) REVERT: B 861 CYS cc_start: 0.3998 (m) cc_final: 0.3560 (m) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1339 time to fit residues: 17.1151 Evaluate side-chains 56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5709 r_free = 0.5709 target = 0.246242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.218291 restraints weight = 43907.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.219397 restraints weight = 38440.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.221710 restraints weight = 31507.996| |-----------------------------------------------------------------------------| r_work (final): 0.5287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0377 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7366 Z= 0.148 Angle : 0.632 6.794 10026 Z= 0.297 Chirality : 0.044 0.157 1218 Planarity : 0.005 0.048 1208 Dihedral : 4.179 18.300 960 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.31), residues: 890 helix: 1.12 (0.23), residues: 575 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 680 HIS 0.007 0.001 HIS B 852 PHE 0.018 0.001 PHE A 489 TYR 0.005 0.001 TYR B 842 ARG 0.001 0.000 ARG A 869 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 861 CYS cc_start: 0.4444 (m) cc_final: 0.4092 (m) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1561 time to fit residues: 19.1878 Evaluate side-chains 57 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5710 r_free = 0.5710 target = 0.246466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.220949 restraints weight = 43279.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5324 r_free = 0.5324 target = 0.222173 restraints weight = 35026.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.222804 restraints weight = 31156.251| |-----------------------------------------------------------------------------| r_work (final): 0.5326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0432 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7366 Z= 0.151 Angle : 0.619 6.565 10026 Z= 0.291 Chirality : 0.043 0.153 1218 Planarity : 0.005 0.047 1208 Dihedral : 4.128 18.425 960 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.31), residues: 890 helix: 1.13 (0.23), residues: 586 sheet: None (None), residues: 0 loop : -1.06 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 680 HIS 0.006 0.001 HIS B 852 PHE 0.021 0.001 PHE B 489 TYR 0.007 0.001 TYR A 842 ARG 0.001 0.000 ARG A 869 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.37 seconds wall clock time: 35 minutes 26.74 seconds (2126.74 seconds total)