Starting phenix.real_space_refine on Wed Mar 4 07:41:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8i_10123/03_2026/6s8i_10123.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7644 2.51 5 N 2076 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12066 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12066 At special positions: 0 Unit cell: (101.88, 98.484, 123.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2295 8.00 N 2076 7.00 C 7644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.00 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.09 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.99 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 548.0 milliseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 12.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.034A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.626A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY H 16 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB6, first strand: chain 'F' and resid 580 through 581 removed outlier: 4.665A pdb=" N LEU E 35 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.754A pdb=" N GLU C 106 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU E 106 " --> pdb=" O CYS E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.595A pdb=" N TRP O 38 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP U 38 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'P' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY P 16 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 3 through 7 removed outlier: 5.892A pdb=" N GLY Y 16 " --> pdb=" O SER Y 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3942 1.34 - 1.46: 2877 1.46 - 1.58: 5481 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 12360 Sorted by residual: bond pdb=" CG LEU Y 99 " pdb=" CD2 LEU Y 99 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CG LEU H 99 " pdb=" CD2 LEU H 99 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CG LEU P 99 " pdb=" CD2 LEU P 99 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.11e+00 bond pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 ... (remaining 12355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 15257 1.50 - 2.99: 1239 2.99 - 4.49: 215 4.49 - 5.99: 65 5.99 - 7.48: 24 Bond angle restraints: 16800 Sorted by residual: angle pdb=" CA TYR U 52 " pdb=" CB TYR U 52 " pdb=" CG TYR U 52 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TYR O 52 " pdb=" CB TYR O 52 " pdb=" CG TYR O 52 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TRP H 107 " pdb=" CB TRP H 107 " pdb=" CG TRP H 107 " ideal model delta sigma weight residual 113.60 120.44 -6.84 1.90e+00 2.77e-01 1.30e+01 angle pdb=" CA TRP Y 107 " pdb=" CB TRP Y 107 " pdb=" CG TRP Y 107 " ideal model delta sigma weight residual 113.60 120.43 -6.83 1.90e+00 2.77e-01 1.29e+01 angle pdb=" CA TYR L 52 " pdb=" CB TYR L 52 " pdb=" CG TYR L 52 " ideal model delta sigma weight residual 113.90 120.37 -6.47 1.80e+00 3.09e-01 1.29e+01 ... (remaining 16795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 6607 17.07 - 34.13: 533 34.13 - 51.20: 174 51.20 - 68.27: 30 68.27 - 85.34: 12 Dihedral angle restraints: 7356 sinusoidal: 2931 harmonic: 4425 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.01 -72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.03 -72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -13.04 -72.96 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 7353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1815 0.193 - 0.387: 12 0.387 - 0.580: 3 0.580 - 0.774: 0 0.774 - 0.967: 3 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-02 2.50e+03 2.34e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-02 2.50e+03 2.33e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-02 2.50e+03 2.32e+03 ... (remaining 1830 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 563 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C ASN B 563 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN B 563 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 564 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 563 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C ASN F 563 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN F 563 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU F 564 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 70 " 0.018 2.00e-02 2.50e+03 1.49e-02 3.87e+00 pdb=" CG PHE H 70 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE H 70 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 70 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 70 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 70 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 70 " 0.003 2.00e-02 2.50e+03 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 644 2.72 - 3.26: 10988 3.26 - 3.81: 17663 3.81 - 4.35: 23182 4.35 - 4.90: 40220 Nonbonded interactions: 92697 Sorted by model distance: nonbonded pdb=" OG1 THR H 100 " pdb=" O ARG H 105 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR P 100 " pdb=" O ARG P 105 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR Y 100 " pdb=" O ARG Y 105 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP L 100 " pdb=" OG1 THR A 144 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" O TYR A 162 " model vdw 2.276 3.040 ... (remaining 92692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 0.065 12387 Z= 0.300 Angle : 1.066 30.216 16860 Z= 0.554 Chirality : 0.073 0.967 1833 Planarity : 0.006 0.042 2187 Dihedral : 14.063 85.336 4491 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 8.13 % Allowed : 7.42 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1536 helix: -0.10 (0.40), residues: 144 sheet: 0.61 (0.20), residues: 573 loop : -0.69 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 54 TYR 0.027 0.003 TYR L 94 PHE 0.034 0.003 PHE Y 70 TRP 0.017 0.002 TRP H 47 HIS 0.008 0.002 HIS U 37 Details of bonding type rmsd covalent geometry : bond 0.00712 (12360) covalent geometry : angle 0.95494 (16800) SS BOND : bond 0.01725 ( 21) SS BOND : angle 1.98840 ( 42) hydrogen bonds : bond 0.15555 ( 447) hydrogen bonds : angle 7.43894 ( 1242) link_BETA1-4 : bond 0.06517 ( 3) link_BETA1-4 : angle 20.03866 ( 9) link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 2.43164 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 260 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: C 56 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7052 (tptt) REVERT: E 56 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6766 (tptt) REVERT: E 156 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8025 (mt-10) REVERT: P 6 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: P 97 TYR cc_start: 0.8407 (m-80) cc_final: 0.8193 (m-80) REVERT: Y 53 SER cc_start: 0.7716 (t) cc_final: 0.7446 (p) outliers start: 102 outliers final: 38 residues processed: 346 average time/residue: 0.4859 time to fit residues: 184.2135 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 TRP Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 107 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN L 82 GLN H 39 GLN A 39 HIS A 61 ASN A 107 ASN A 188 GLN B 516 HIS C 39 HIS C 61 ASN C 107 ASN E 39 HIS E 61 ASN E 107 ASN O 40 GLN O 41 GLN O 82 GLN U 40 GLN U 82 GLN P 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.185111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150536 restraints weight = 13662.036| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.30 r_work: 0.3323 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12387 Z= 0.185 Angle : 0.730 7.074 16860 Z= 0.374 Chirality : 0.049 0.378 1833 Planarity : 0.005 0.037 2187 Dihedral : 8.102 57.082 1896 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.78 % Allowed : 16.27 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1536 helix: 1.64 (0.48), residues: 126 sheet: 0.64 (0.20), residues: 579 loop : -0.53 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 596 TYR 0.020 0.002 TYR U 52 PHE 0.016 0.002 PHE H 70 TRP 0.014 0.002 TRP Y 47 HIS 0.006 0.002 HIS U 37 Details of bonding type rmsd covalent geometry : bond 0.00429 (12360) covalent geometry : angle 0.71545 (16800) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.44329 ( 42) hydrogen bonds : bond 0.05956 ( 447) hydrogen bonds : angle 5.73328 ( 1242) link_BETA1-4 : bond 0.00779 ( 3) link_BETA1-4 : angle 3.25801 ( 9) link_NAG-ASN : bond 0.02070 ( 3) link_NAG-ASN : angle 4.76618 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 186 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8710 (p90) cc_final: 0.7367 (p90) REVERT: H 6 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6707 (mt-10) REVERT: H 43 LYS cc_start: 0.7687 (tppt) cc_final: 0.7439 (mptp) REVERT: A 140 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7472 (mtpp) REVERT: B 547 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (tt) REVERT: D 547 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8197 (tt) REVERT: F 596 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7455 (mmt90) REVERT: C 56 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6862 (tptt) REVERT: C 219 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: E 56 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6604 (tptt) REVERT: E 140 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7650 (mtpp) REVERT: O 10 SER cc_start: 0.7531 (OUTLIER) cc_final: 0.7291 (m) REVERT: P 6 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: Y 106 TYR cc_start: 0.8056 (m-80) cc_final: 0.7840 (m-10) outliers start: 85 outliers final: 44 residues processed: 248 average time/residue: 0.5906 time to fit residues: 158.5558 Evaluate side-chains 227 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain Y residue 19 ARG Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 516 HIS C 61 ASN E 61 ASN U 41 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139373 restraints weight = 14134.503| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.33 r_work: 0.3205 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12387 Z= 0.231 Angle : 0.741 7.360 16860 Z= 0.386 Chirality : 0.050 0.402 1833 Planarity : 0.006 0.044 2187 Dihedral : 7.615 59.867 1873 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 7.18 % Allowed : 16.51 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1536 helix: 1.42 (0.48), residues: 126 sheet: 0.46 (0.20), residues: 597 loop : -0.89 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 596 TYR 0.018 0.002 TYR L 34 PHE 0.015 0.002 PHE E 225 TRP 0.016 0.002 TRP H 47 HIS 0.006 0.002 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00562 (12360) covalent geometry : angle 0.72873 (16800) SS BOND : bond 0.00244 ( 21) SS BOND : angle 1.44702 ( 42) hydrogen bonds : bond 0.05785 ( 447) hydrogen bonds : angle 5.55486 ( 1242) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 2.74032 ( 9) link_NAG-ASN : bond 0.02645 ( 3) link_NAG-ASN : angle 4.48056 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 165 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8901 (p90) cc_final: 0.7564 (p90) REVERT: H 6 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: H 43 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7560 (mptp) REVERT: A 66 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 140 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7607 (mtpp) REVERT: B 547 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8261 (tp) REVERT: C 54 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6371 (tpm170) REVERT: C 56 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6991 (tptp) REVERT: C 219 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6764 (mtp180) REVERT: E 56 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6834 (tptt) REVERT: E 140 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7690 (mtpp) REVERT: O 100 ASP cc_start: 0.7768 (m-30) cc_final: 0.7467 (m-30) REVERT: P 6 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7160 (mt-10) outliers start: 90 outliers final: 56 residues processed: 230 average time/residue: 0.5270 time to fit residues: 132.0114 Evaluate side-chains 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147786 restraints weight = 13939.203| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.73 r_work: 0.3332 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12387 Z= 0.118 Angle : 0.598 6.955 16860 Z= 0.306 Chirality : 0.046 0.438 1833 Planarity : 0.004 0.038 2187 Dihedral : 6.866 55.994 1870 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.39 % Allowed : 18.82 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1536 helix: 1.48 (0.49), residues: 126 sheet: 0.63 (0.21), residues: 537 loop : -0.74 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 596 TYR 0.012 0.001 TYR L 52 PHE 0.013 0.001 PHE E 225 TRP 0.009 0.001 TRP Y 47 HIS 0.002 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00252 (12360) covalent geometry : angle 0.58401 (16800) SS BOND : bond 0.00240 ( 21) SS BOND : angle 1.16411 ( 42) hydrogen bonds : bond 0.04169 ( 447) hydrogen bonds : angle 5.14962 ( 1242) link_BETA1-4 : bond 0.00346 ( 3) link_BETA1-4 : angle 2.16054 ( 9) link_NAG-ASN : bond 0.02158 ( 3) link_NAG-ASN : angle 4.60718 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7618 (mptp) REVERT: A 54 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.6101 (mpt180) REVERT: A 140 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7473 (mtpm) REVERT: B 514 ASN cc_start: 0.8319 (m110) cc_final: 0.8079 (m-40) REVERT: C 56 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.7004 (tptp) REVERT: E 56 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6851 (tptt) REVERT: E 140 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7610 (mtpm) REVERT: E 219 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7226 (mtp180) REVERT: O 7 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6264 (mt0) REVERT: O 10 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7401 (m) REVERT: O 100 ASP cc_start: 0.7658 (m-30) cc_final: 0.7326 (m-30) outliers start: 55 outliers final: 29 residues processed: 211 average time/residue: 0.5955 time to fit residues: 135.8667 Evaluate side-chains 198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 0.0020 chunk 64 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN A 61 ASN C 61 ASN C 188 GLN E 61 ASN E 188 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149026 restraints weight = 13774.511| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.58 r_work: 0.3265 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12387 Z= 0.140 Angle : 0.608 6.978 16860 Z= 0.312 Chirality : 0.046 0.408 1833 Planarity : 0.004 0.042 2187 Dihedral : 6.472 53.745 1859 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.66 % Allowed : 18.10 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1536 helix: 1.40 (0.48), residues: 126 sheet: 0.56 (0.21), residues: 543 loop : -0.76 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 596 TYR 0.012 0.001 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.011 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00324 (12360) covalent geometry : angle 0.59615 (16800) SS BOND : bond 0.00241 ( 21) SS BOND : angle 1.13373 ( 42) hydrogen bonds : bond 0.04356 ( 447) hydrogen bonds : angle 5.03191 ( 1242) link_BETA1-4 : bond 0.00293 ( 3) link_BETA1-4 : angle 2.29154 ( 9) link_NAG-ASN : bond 0.02098 ( 3) link_NAG-ASN : angle 4.18316 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 161 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7520 (mptp) REVERT: A 54 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.6091 (mpt180) REVERT: A 140 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7522 (mtpm) REVERT: B 514 ASN cc_start: 0.8366 (m110) cc_final: 0.8131 (m-40) REVERT: B 547 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8293 (tt) REVERT: B 564 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7831 (tt0) REVERT: D 547 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 54 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6232 (tpm170) REVERT: C 112 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: E 140 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7657 (mtpp) REVERT: O 7 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6149 (mt0) REVERT: O 10 SER cc_start: 0.7537 (OUTLIER) cc_final: 0.7325 (m) REVERT: O 100 ASP cc_start: 0.7757 (m-30) cc_final: 0.7539 (m-30) outliers start: 71 outliers final: 48 residues processed: 204 average time/residue: 0.5888 time to fit residues: 129.7029 Evaluate side-chains 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 125 optimal weight: 0.0270 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN C 228 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.183509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148486 restraints weight = 13900.173| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.59 r_work: 0.3342 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12387 Z= 0.131 Angle : 0.593 7.368 16860 Z= 0.303 Chirality : 0.045 0.414 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.996 53.097 1850 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.78 % Allowed : 19.46 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1536 helix: 1.46 (0.49), residues: 126 sheet: 0.52 (0.21), residues: 543 loop : -0.73 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 596 TYR 0.011 0.001 TYR U 52 PHE 0.013 0.001 PHE A 225 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00300 (12360) covalent geometry : angle 0.58067 (16800) SS BOND : bond 0.00230 ( 21) SS BOND : angle 1.12170 ( 42) hydrogen bonds : bond 0.04146 ( 447) hydrogen bonds : angle 4.92365 ( 1242) link_BETA1-4 : bond 0.00321 ( 3) link_BETA1-4 : angle 2.27903 ( 9) link_NAG-ASN : bond 0.02051 ( 3) link_NAG-ASN : angle 4.25184 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7489 (mmm160) REVERT: H 43 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7498 (mptp) REVERT: A 54 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5900 (tpm170) REVERT: A 140 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7555 (mtpm) REVERT: B 514 ASN cc_start: 0.8385 (m110) cc_final: 0.8148 (m-40) REVERT: B 547 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8293 (tt) REVERT: B 564 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7929 (tt0) REVERT: D 596 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7439 (mmt90) REVERT: C 54 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6217 (tpm170) REVERT: C 112 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: E 140 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7598 (mtpm) REVERT: O 7 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6161 (mt0) REVERT: O 10 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.7355 (m) REVERT: O 100 ASP cc_start: 0.7715 (m-30) cc_final: 0.7486 (m-30) outliers start: 60 outliers final: 45 residues processed: 194 average time/residue: 0.6363 time to fit residues: 133.4117 Evaluate side-chains 204 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN P 54 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.145247 restraints weight = 14051.068| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.63 r_work: 0.3328 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12387 Z= 0.157 Angle : 0.627 11.094 16860 Z= 0.318 Chirality : 0.047 0.412 1833 Planarity : 0.004 0.044 2187 Dihedral : 6.000 53.910 1848 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.26 % Allowed : 19.38 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1536 helix: 1.45 (0.48), residues: 126 sheet: 0.40 (0.20), residues: 564 loop : -0.86 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.012 0.001 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00374 (12360) covalent geometry : angle 0.60766 (16800) SS BOND : bond 0.00236 ( 21) SS BOND : angle 1.13572 ( 42) hydrogen bonds : bond 0.04501 ( 447) hydrogen bonds : angle 4.95218 ( 1242) link_BETA1-4 : bond 0.00651 ( 3) link_BETA1-4 : angle 2.22669 ( 9) link_NAG-ASN : bond 0.01745 ( 3) link_NAG-ASN : angle 5.97580 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7409 (mmm160) REVERT: H 43 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7500 (mptp) REVERT: A 54 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5955 (tpm170) REVERT: A 140 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7570 (mtpm) REVERT: B 514 ASN cc_start: 0.8417 (m110) cc_final: 0.8190 (m-40) REVERT: B 547 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8316 (tt) REVERT: B 564 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7924 (tt0) REVERT: D 547 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 54 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6217 (tpm170) REVERT: C 112 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: E 140 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7610 (mtpm) REVERT: O 7 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6175 (mt0) outliers start: 66 outliers final: 51 residues processed: 192 average time/residue: 0.6044 time to fit residues: 125.4857 Evaluate side-chains 210 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 123 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.177169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139295 restraints weight = 13981.860| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.91 r_work: 0.3220 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12387 Z= 0.200 Angle : 0.673 9.553 16860 Z= 0.344 Chirality : 0.048 0.404 1833 Planarity : 0.005 0.046 2187 Dihedral : 6.212 57.499 1847 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.14 % Allowed : 18.82 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1536 helix: 1.29 (0.49), residues: 126 sheet: 0.47 (0.20), residues: 594 loop : -1.02 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 596 TYR 0.016 0.002 TYR U 52 PHE 0.015 0.002 PHE A 225 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS U 37 Details of bonding type rmsd covalent geometry : bond 0.00488 (12360) covalent geometry : angle 0.65622 (16800) SS BOND : bond 0.00276 ( 21) SS BOND : angle 1.21262 ( 42) hydrogen bonds : bond 0.05109 ( 447) hydrogen bonds : angle 5.12692 ( 1242) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 2.48579 ( 9) link_NAG-ASN : bond 0.01752 ( 3) link_NAG-ASN : angle 5.60703 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 153 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7392 (mmm160) REVERT: H 43 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7407 (mptp) REVERT: A 54 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5999 (tpm170) REVERT: A 140 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7638 (mtpm) REVERT: B 514 ASN cc_start: 0.8435 (m110) cc_final: 0.8222 (m-40) REVERT: B 547 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 564 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7963 (tt0) REVERT: D 547 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8311 (tt) REVERT: C 54 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6249 (tpm170) REVERT: C 112 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: E 140 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7683 (mtpp) REVERT: O 7 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6241 (mt0) outliers start: 77 outliers final: 55 residues processed: 201 average time/residue: 0.6306 time to fit residues: 136.7140 Evaluate side-chains 207 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 228 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.178139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140579 restraints weight = 13983.020| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.93 r_work: 0.3244 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12387 Z= 0.130 Angle : 0.606 10.787 16860 Z= 0.306 Chirality : 0.046 0.428 1833 Planarity : 0.004 0.047 2187 Dihedral : 5.951 55.095 1847 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.78 % Allowed : 20.33 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1536 helix: 1.50 (0.49), residues: 126 sheet: 0.43 (0.21), residues: 540 loop : -0.88 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 596 TYR 0.012 0.001 TYR U 52 PHE 0.013 0.001 PHE A 225 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00299 (12360) covalent geometry : angle 0.58624 (16800) SS BOND : bond 0.00213 ( 21) SS BOND : angle 1.08715 ( 42) hydrogen bonds : bond 0.04108 ( 447) hydrogen bonds : angle 4.88649 ( 1242) link_BETA1-4 : bond 0.00450 ( 3) link_BETA1-4 : angle 2.27393 ( 9) link_NAG-ASN : bond 0.01795 ( 3) link_NAG-ASN : angle 6.01831 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7456 (mptp) REVERT: A 54 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.6026 (tpm170) REVERT: A 140 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7573 (mtpm) REVERT: B 514 ASN cc_start: 0.8423 (m110) cc_final: 0.8206 (m-40) REVERT: B 547 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8313 (tt) REVERT: C 54 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6250 (tpm170) REVERT: C 112 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: E 140 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7645 (mtpm) REVERT: E 219 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7287 (mtp180) REVERT: O 7 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6182 (mt0) outliers start: 60 outliers final: 41 residues processed: 200 average time/residue: 0.5984 time to fit residues: 129.9343 Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 0.0050 chunk 98 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN E 62 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.181795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144372 restraints weight = 13944.452| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.74 r_work: 0.3252 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12387 Z= 0.134 Angle : 0.613 10.279 16860 Z= 0.308 Chirality : 0.046 0.413 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.931 54.590 1847 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.31 % Allowed : 21.13 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1536 helix: 1.54 (0.49), residues: 126 sheet: 0.49 (0.21), residues: 552 loop : -0.93 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.011 0.001 TYR U 52 PHE 0.013 0.001 PHE A 225 TRP 0.011 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00310 (12360) covalent geometry : angle 0.59347 (16800) SS BOND : bond 0.00227 ( 21) SS BOND : angle 1.13576 ( 42) hydrogen bonds : bond 0.04103 ( 447) hydrogen bonds : angle 4.82815 ( 1242) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 2.37400 ( 9) link_NAG-ASN : bond 0.01707 ( 3) link_NAG-ASN : angle 5.85222 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7519 (mptp) REVERT: A 54 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.6031 (tpm170) REVERT: A 140 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7614 (mtpm) REVERT: B 514 ASN cc_start: 0.8434 (m110) cc_final: 0.8218 (m-40) REVERT: B 547 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (tt) REVERT: C 54 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6263 (tpm170) REVERT: C 112 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: E 140 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7627 (mtpm) REVERT: O 7 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6180 (mt0) outliers start: 54 outliers final: 42 residues processed: 185 average time/residue: 0.5904 time to fit residues: 118.2053 Evaluate side-chains 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 109 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 61 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.174222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135365 restraints weight = 14102.144| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.38 r_work: 0.3225 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12387 Z= 0.228 Angle : 0.707 10.064 16860 Z= 0.360 Chirality : 0.049 0.393 1833 Planarity : 0.005 0.046 2187 Dihedral : 6.243 58.545 1846 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.94 % Allowed : 20.41 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1536 helix: 1.25 (0.49), residues: 126 sheet: 0.44 (0.20), residues: 594 loop : -1.12 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 596 TYR 0.017 0.002 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS U 37 Details of bonding type rmsd covalent geometry : bond 0.00557 (12360) covalent geometry : angle 0.69033 (16800) SS BOND : bond 0.00279 ( 21) SS BOND : angle 1.27563 ( 42) hydrogen bonds : bond 0.05356 ( 447) hydrogen bonds : angle 5.18285 ( 1242) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 2.63892 ( 9) link_NAG-ASN : bond 0.01818 ( 3) link_NAG-ASN : angle 5.57954 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.60 seconds wall clock time: 63 minutes 33.23 seconds (3813.23 seconds total)