Starting phenix.real_space_refine on Thu Apr 11 10:09:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/04_2024/8gcc_29930_updated.pdb" } resolution = 2.94 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= 0.065 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: 7 Type Number sf(0) Gaussians P 48 5.49 5 S 36 5.16 5 C 7393 2.51 5 N 2064 2.21 5 O 2158 1.98 5 F 6 1.80 5 H 10631 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10371 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 18, 'GLU:plan': 30, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 10379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10379 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 18, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.03, per 1000 atoms: 0.45 Number of scatterers: 22336 At special positions: 0 Unit cell: (93.795, 109.005, 114.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 48 15.00 F 6 9.00 O 2158 8.00 N 2064 7.00 C 7393 6.00 H 10631 1.00 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.88 Conformation dependent library (CDL) restraints added in 2.3 seconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 10 sheets defined 46.5% alpha, 6.4% beta 24 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 13.41 Creating SS restraints... Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.639A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 569 through 585 removed outlier: 6.204A pdb=" N ASP A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 584 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 636 through 647 Processing helix chain 'A' and resid 665 through 684 removed outlier: 4.913A pdb=" N ILE A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 784 through 787 No H-bonds generated for 'chain 'A' and resid 784 through 787' Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 902 through 914 Processing helix chain 'A' and resid 938 through 947 Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 980 through 1024 Processing helix chain 'A' and resid 1035 through 1044 Processing helix chain 'A' and resid 1104 through 1110 Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1124 through 1146 removed outlier: 3.564A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1176 Proline residue: A1162 - end of helix Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 437 through 448 removed outlier: 3.633A pdb=" N ALA B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 478 through 487 Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 532 through 535 No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 569 through 585 removed outlier: 6.217A pdb=" N ASP B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 584 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN B 585 " --> pdb=" O ASP B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 622 through 630 Processing helix chain 'B' and resid 636 through 647 Processing helix chain 'B' and resid 665 through 684 removed outlier: 4.918A pdb=" N ILE B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 705 Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 731 through 742 Processing helix chain 'B' and resid 784 through 787 No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 791 through 794 Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 902 through 914 Processing helix chain 'B' and resid 938 through 947 Processing helix chain 'B' and resid 950 through 953 No H-bonds generated for 'chain 'B' and resid 950 through 953' Processing helix chain 'B' and resid 980 through 1025 Processing helix chain 'B' and resid 1035 through 1044 Processing helix chain 'B' and resid 1104 through 1110 Processing helix chain 'B' and resid 1112 through 1115 No H-bonds generated for 'chain 'B' and resid 1112 through 1115' Processing helix chain 'B' and resid 1119 through 1121 No H-bonds generated for 'chain 'B' and resid 1119 through 1121' Processing helix chain 'B' and resid 1124 through 1146 removed outlier: 3.567A pdb=" N LYS B1146 " --> pdb=" O ALA B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1176 Proline residue: B1162 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 454 through 456 removed outlier: 6.510A pdb=" N THR A 429 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS A 505 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 754 through 757 Processing sheet with id= C, first strand: chain 'A' and resid 957 through 961 removed outlier: 6.502A pdb=" N VAL A 878 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 871 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 880 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 869 " --> pdb=" O THR A 880 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 883 through 885 Processing sheet with id= E, first strand: chain 'A' and resid 965 through 968 removed outlier: 4.328A pdb=" N ILE A 965 " --> pdb=" O TYR A 977 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.589A pdb=" N THR B 429 " --> pdb=" O GLY B 455 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS B 505 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 754 through 757 Processing sheet with id= H, first strand: chain 'B' and resid 957 through 961 removed outlier: 6.355A pdb=" N VAL B 878 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B 871 " --> pdb=" O VAL B 878 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 880 " --> pdb=" O ILE B 869 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE B 869 " --> pdb=" O THR B 880 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 883 through 885 Processing sheet with id= J, first strand: chain 'B' and resid 965 through 968 removed outlier: 4.327A pdb=" N ILE B 965 " --> pdb=" O TYR B 977 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 9.00 Time building geometry restraints manager: 19.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10623 1.03 - 1.23: 50 1.23 - 1.42: 5178 1.42 - 1.62: 6781 1.62 - 1.81: 62 Bond restraints: 22694 Sorted by residual: bond pdb=" C17 YWX C 101 " pdb=" C6 YWX C 101 " ideal model delta sigma weight residual 1.154 1.395 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C17 YWX D 101 " pdb=" C6 YWX D 101 " ideal model delta sigma weight residual 1.154 1.394 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C5 YWX D 101 " pdb=" C6 YWX D 101 " ideal model delta sigma weight residual 1.285 1.521 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C5 YWX C 101 " pdb=" C6 YWX C 101 " ideal model delta sigma weight residual 1.285 1.519 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C17 YWX D 101 " pdb=" C18 YWX D 101 " ideal model delta sigma weight residual 1.285 1.501 -0.216 2.00e-02 2.50e+03 1.16e+02 ... (remaining 22689 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 527 106.34 - 113.25: 25286 113.25 - 120.16: 7677 120.16 - 127.07: 7103 127.07 - 133.98: 229 Bond angle restraints: 40822 Sorted by residual: angle pdb=" C10 YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F1 YWX D 101 " ideal model delta sigma weight residual 80.33 112.65 -32.32 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YWX C 101 " pdb=" C15 YWX C 101 " pdb=" F1 YWX C 101 " ideal model delta sigma weight residual 80.33 112.62 -32.29 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F2 YWX D 101 " ideal model delta sigma weight residual 80.33 112.46 -32.13 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C10 YWX C 101 " pdb=" C15 YWX C 101 " pdb=" F2 YWX C 101 " ideal model delta sigma weight residual 80.33 112.42 -32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" F YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F2 YWX D 101 " ideal model delta sigma weight residual 80.32 106.35 -26.03 3.00e+00 1.11e-01 7.53e+01 ... (remaining 40817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 10005 34.81 - 69.62: 542 69.62 - 104.43: 21 104.43 - 139.24: 0 139.24 - 174.05: 2 Dihedral angle restraints: 10570 sinusoidal: 5688 harmonic: 4882 Sorted by residual: dihedral pdb=" C4' DA C 3 " pdb=" C3' DA C 3 " pdb=" O3' DA C 3 " pdb=" P DT C 4 " ideal model delta sinusoidal sigma weight residual 220.00 45.95 174.05 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG C 2 " pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DA C 3 " ideal model delta sinusoidal sigma weight residual 220.00 73.89 146.11 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASP A 615 " pdb=" CB ASP A 615 " pdb=" CG ASP A 615 " pdb=" OD1 ASP A 615 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1152 0.027 - 0.055: 434 0.055 - 0.082: 169 0.082 - 0.109: 78 0.109 - 0.137: 31 Chirality restraints: 1864 Sorted by residual: chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 893 " pdb=" N ILE B 893 " pdb=" C ILE B 893 " pdb=" CB ILE B 893 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 966 " pdb=" N ILE A 966 " pdb=" C ILE A 966 " pdb=" CB ILE A 966 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1861 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C YWX D 101 " -0.049 2.00e-02 2.50e+03 8.07e-02 2.12e+02 pdb=" O YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C1 YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C16 YWX D 101 " 0.069 2.00e-02 2.50e+03 pdb=" C17 YWX D 101 " 0.092 2.00e-02 2.50e+03 pdb=" C18 YWX D 101 " 0.118 2.00e-02 2.50e+03 pdb=" C5 YWX D 101 " 0.096 2.00e-02 2.50e+03 pdb=" C6 YWX D 101 " 0.050 2.00e-02 2.50e+03 pdb=" C7 YWX D 101 " -0.054 2.00e-02 2.50e+03 pdb=" C8 YWX D 101 " -0.018 2.00e-02 2.50e+03 pdb=" C9 YWX D 101 " -0.134 2.00e-02 2.50e+03 pdb=" N4 YWX D 101 " 0.048 2.00e-02 2.50e+03 pdb=" N5 YWX D 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C YWX C 101 " 0.010 2.00e-02 2.50e+03 2.31e-02 1.74e+01 pdb=" O YWX C 101 " 0.015 2.00e-02 2.50e+03 pdb=" C1 YWX C 101 " 0.030 2.00e-02 2.50e+03 pdb=" C16 YWX C 101 " -0.036 2.00e-02 2.50e+03 pdb=" C17 YWX C 101 " -0.032 2.00e-02 2.50e+03 pdb=" C18 YWX C 101 " -0.018 2.00e-02 2.50e+03 pdb=" C5 YWX C 101 " -0.016 2.00e-02 2.50e+03 pdb=" C6 YWX C 101 " -0.012 2.00e-02 2.50e+03 pdb=" C7 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C8 YWX C 101 " -0.006 2.00e-02 2.50e+03 pdb=" C9 YWX C 101 " 0.049 2.00e-02 2.50e+03 pdb=" N4 YWX C 101 " -0.007 2.00e-02 2.50e+03 pdb=" N5 YWX C 101 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N YWX C 101 " 0.033 2.00e-02 2.50e+03 2.98e-02 1.55e+01 pdb=" C1 YWX C 101 " -0.048 2.00e-02 2.50e+03 pdb=" C2 YWX C 101 " 0.002 2.00e-02 2.50e+03 pdb=" C3 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C4 YWX C 101 " -0.027 2.00e-02 2.50e+03 pdb=" N1 YWX C 101 " 0.042 2.00e-02 2.50e+03 pdb=" N2 YWX C 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1043 2.17 - 2.78: 41804 2.78 - 3.38: 62690 3.38 - 3.99: 84583 3.99 - 4.60: 130939 Nonbonded interactions: 321059 Sorted by model distance: nonbonded pdb=" O ARG A 451 " pdb="HH11 ARG A 451 " model vdw 1.560 1.850 nonbonded pdb=" O ARG B 451 " pdb="HH11 ARG B 451 " model vdw 1.560 1.850 nonbonded pdb=" HH TYR A 995 " pdb=" OD2 ASP A1156 " model vdw 1.586 1.850 nonbonded pdb=" HH TYR B 995 " pdb=" OD2 ASP B1156 " model vdw 1.587 1.850 nonbonded pdb=" O ALA B 632 " pdb="HH22 ARG B 639 " model vdw 1.599 1.850 ... (remaining 321054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 409 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name NE or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 1119 through 1177)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.350 Extract box with map and model: 13.040 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 83.170 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 0.241 12063 Z= 0.396 Angle : 1.038 32.318 16582 Z= 0.417 Chirality : 0.039 0.137 1864 Planarity : 0.004 0.081 1949 Dihedral : 20.020 174.051 4344 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 18.17 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1402 helix: 2.65 (0.21), residues: 672 sheet: -1.56 (0.44), residues: 158 loop : -0.19 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.011 0.001 TYR B1111 ARG 0.002 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 25 residues processed: 131 average time/residue: 2.2014 time to fit residues: 318.3813 Evaluate side-chains 125 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12063 Z= 0.265 Angle : 0.740 23.856 16582 Z= 0.332 Chirality : 0.039 0.136 1864 Planarity : 0.003 0.037 1949 Dihedral : 17.906 174.196 2132 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.25 % Allowed : 17.56 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1402 helix: 2.47 (0.20), residues: 688 sheet: -1.40 (0.45), residues: 154 loop : -0.22 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE A 676 TYR 0.009 0.001 TYR B 994 ARG 0.004 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7836 (p0) cc_final: 0.7632 (p0) REVERT: B 657 ASN cc_start: 0.7788 (p0) cc_final: 0.7583 (p0) REVERT: B 1140 GLU cc_start: 0.7782 (tp30) cc_final: 0.7377 (tp30) outliers start: 32 outliers final: 12 residues processed: 141 average time/residue: 2.0329 time to fit residues: 319.3528 Evaluate side-chains 117 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 920 GLN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12063 Z= 0.206 Angle : 0.725 23.790 16582 Z= 0.324 Chirality : 0.038 0.137 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.690 174.549 2112 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.64 % Allowed : 17.56 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1402 helix: 2.65 (0.21), residues: 688 sheet: -1.63 (0.47), residues: 134 loop : -0.19 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.002 0.001 HIS B 612 PHE 0.010 0.001 PHE A 676 TYR 0.007 0.001 TYR A 994 ARG 0.003 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7874 (p0) cc_final: 0.7651 (p0) REVERT: A 723 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: A 1044 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7008 (mp-120) REVERT: B 723 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: B 1140 GLU cc_start: 0.7771 (tp30) cc_final: 0.7371 (tp30) outliers start: 26 outliers final: 13 residues processed: 137 average time/residue: 2.0759 time to fit residues: 316.1577 Evaluate side-chains 121 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12063 Z= 0.196 Angle : 0.719 23.866 16582 Z= 0.320 Chirality : 0.038 0.136 1864 Planarity : 0.003 0.030 1949 Dihedral : 17.656 174.544 2112 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.23 % Allowed : 18.27 % Favored : 79.49 % 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: 1.67 (0.24), residues: 1402 helix: 2.71 (0.21), residues: 688 sheet: -1.59 (0.46), residues: 134 loop : -0.18 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 612 PHE 0.010 0.001 PHE B 676 TYR 0.007 0.001 TYR B 994 ARG 0.002 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7878 (p0) cc_final: 0.7650 (p0) REVERT: A 1044 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7056 (mp-120) REVERT: B 1140 GLU cc_start: 0.7765 (tp30) cc_final: 0.7384 (tp30) outliers start: 22 outliers final: 12 residues processed: 136 average time/residue: 2.0707 time to fit residues: 313.4090 Evaluate side-chains 123 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12063 Z= 0.328 Angle : 0.753 23.705 16582 Z= 0.342 Chirality : 0.040 0.138 1864 Planarity : 0.004 0.030 1949 Dihedral : 17.786 173.240 2107 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.05 % Allowed : 17.66 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1402 helix: 2.49 (0.20), residues: 684 sheet: -1.47 (0.44), residues: 154 loop : -0.33 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.004 0.001 HIS B 612 PHE 0.012 0.001 PHE A 676 TYR 0.010 0.001 TYR B 994 ARG 0.001 0.000 ARG B1118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 2.910 Fit side-chains revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7925 (p0) cc_final: 0.7660 (p0) REVERT: A 723 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: B 723 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: B 1044 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7117 (mp-120) outliers start: 30 outliers final: 11 residues processed: 144 average time/residue: 2.0911 time to fit residues: 336.0642 Evaluate side-chains 123 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12063 Z= 0.225 Angle : 0.732 23.841 16582 Z= 0.328 Chirality : 0.039 0.136 1864 Planarity : 0.003 0.027 1949 Dihedral : 17.718 173.856 2104 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.13 % Allowed : 18.98 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1402 helix: 2.63 (0.20), residues: 684 sheet: -1.35 (0.46), residues: 144 loop : -0.28 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.002 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.008 0.001 TYR A 994 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7945 (p0) cc_final: 0.7675 (p0) outliers start: 21 outliers final: 12 residues processed: 131 average time/residue: 2.1139 time to fit residues: 307.9987 Evaluate side-chains 119 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12063 Z= 0.361 Angle : 0.763 23.666 16582 Z= 0.348 Chirality : 0.041 0.141 1864 Planarity : 0.004 0.032 1949 Dihedral : 17.828 172.744 2103 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.94 % Allowed : 18.68 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1402 helix: 2.36 (0.20), residues: 684 sheet: -1.58 (0.45), residues: 144 loop : -0.39 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 642 HIS 0.005 0.001 HIS B 612 PHE 0.012 0.001 PHE A 676 TYR 0.011 0.002 TYR B 994 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7964 (p0) cc_final: 0.7653 (p0) REVERT: A 723 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: A 1139 ASP cc_start: 0.7846 (m-30) cc_final: 0.7505 (m-30) REVERT: B 656 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7719 (ttm) REVERT: B 723 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: B 1044 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7123 (mp-120) outliers start: 29 outliers final: 13 residues processed: 141 average time/residue: 2.1533 time to fit residues: 336.1220 Evaluate side-chains 126 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A1166 ASN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12063 Z= 0.168 Angle : 0.722 23.907 16582 Z= 0.322 Chirality : 0.038 0.136 1864 Planarity : 0.003 0.025 1949 Dihedral : 17.679 174.050 2103 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.52 % Allowed : 19.90 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1402 helix: 2.74 (0.21), residues: 684 sheet: -1.72 (0.48), residues: 124 loop : -0.27 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 642 HIS 0.002 0.000 HIS B 724 PHE 0.009 0.001 PHE A 676 TYR 0.007 0.001 TYR B1111 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7909 (p0) cc_final: 0.7624 (p0) REVERT: B 1044 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7040 (mp-120) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 2.3271 time to fit residues: 337.8775 Evaluate side-chains 121 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1044 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 505 HIS B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12063 Z= 0.237 Angle : 0.734 23.744 16582 Z= 0.330 Chirality : 0.039 0.136 1864 Planarity : 0.003 0.026 1949 Dihedral : 17.676 173.392 2099 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.62 % Allowed : 19.70 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1402 helix: 2.70 (0.20), residues: 684 sheet: -1.77 (0.48), residues: 124 loop : -0.30 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.008 0.001 TYR B 994 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7934 (p0) cc_final: 0.7652 (p0) REVERT: B 1044 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7043 (mp-120) outliers start: 16 outliers final: 13 residues processed: 132 average time/residue: 2.2879 time to fit residues: 332.3055 Evaluate side-chains 123 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12063 Z= 0.240 Angle : 0.735 23.766 16582 Z= 0.330 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.026 1949 Dihedral : 17.675 173.314 2099 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.42 % Allowed : 20.10 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1402 helix: 2.69 (0.21), residues: 684 sheet: -1.79 (0.48), residues: 124 loop : -0.29 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.009 0.001 TYR B1111 ARG 0.002 0.000 ARG A 970 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.7915 (p0) cc_final: 0.7609 (p0) REVERT: B 1044 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7057 (mp-120) outliers start: 14 outliers final: 13 residues processed: 126 average time/residue: 2.0713 time to fit residues: 290.2683 Evaluate side-chains 123 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN A1166 ASN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121099 restraints weight = 37088.628| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.41 r_work: 0.3263 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12063 Z= 0.244 Angle : 0.736 23.764 16582 Z= 0.331 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.027 1949 Dihedral : 17.680 173.318 2099 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.42 % Allowed : 20.10 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1402 helix: 2.68 (0.21), residues: 684 sheet: -1.80 (0.48), residues: 124 loop : -0.28 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE A 676 TYR 0.008 0.001 TYR B 994 ARG 0.002 0.000 ARG A 970 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7362.83 seconds wall clock time: 130 minutes 53.43 seconds (7853.43 seconds total)