Starting phenix.real_space_refine on Wed Jul 30 03:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8i_10123/07_2025/6s8i_10123.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8i_10123/07_2025/6s8i_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_10123/07_2025/6s8i_10123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8i_10123/07_2025/6s8i_10123.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8i_10123/07_2025/6s8i_10123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8i_10123/07_2025/6s8i_10123.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: D, F, I, J, C, E, O, U, P, Y Time building chain proxies: 6.26, per 1000 atoms: 0.52 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.78 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: 4.11 Time building geometry restraints manager: 3.79 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } 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: 1.010 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:16.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.017 0.002 TRP H 47 HIS 0.008 0.002 HIS U 37 PHE 0.034 0.003 PHE Y 70 TYR 0.027 0.003 TYR L 94 ARG 0.015 0.001 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 3) link_NAG-ASN : angle 2.43164 ( 9) link_BETA1-4 : bond 0.06517 ( 3) link_BETA1-4 : angle 20.03866 ( 9) hydrogen bonds : bond 0.15555 ( 447) hydrogen bonds : angle 7.43894 ( 1242) SS BOND : bond 0.01725 ( 21) SS BOND : angle 1.98840 ( 42) covalent geometry : bond 0.00712 (12360) covalent geometry : angle 0.95494 (16800) *********************** 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 : 1.275 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: 0.7051 (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: 0.7447 (p) outliers start: 102 outliers final: 38 residues processed: 346 average time/residue: 1.0080 time to fit residues: 383.0835 Evaluate side-chains 211 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 129 optimal weight: 4.9990 chunk 115 optimal weight: 0.0010 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.186028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149635 restraints weight = 13814.488| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.55 r_work: 0.3282 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12387 Z= 0.153 Angle : 0.695 7.661 16860 Z= 0.355 Chirality : 0.049 0.472 1833 Planarity : 0.005 0.038 2187 Dihedral : 7.958 58.261 1896 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.62 % Allowed : 15.79 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1536 helix: 0.85 (0.46), residues: 144 sheet: 0.72 (0.20), residues: 573 loop : -0.42 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 47 HIS 0.005 0.002 HIS U 37 PHE 0.015 0.002 PHE H 70 TYR 0.018 0.002 TYR U 52 ARG 0.008 0.000 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01033 ( 3) link_NAG-ASN : angle 4.81298 ( 9) link_BETA1-4 : bond 0.00095 ( 3) link_BETA1-4 : angle 3.59885 ( 9) hydrogen bonds : bond 0.05552 ( 447) hydrogen bonds : angle 5.65274 ( 1242) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.58912 ( 42) covalent geometry : bond 0.00334 (12360) covalent geometry : angle 0.67736 (16800) *********************** 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 270 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: H 43 LYS cc_start: 0.7615 (tppt) cc_final: 0.7382 (mptp) REVERT: A 140 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7423 (mtpp) REVERT: B 547 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8295 (tt) REVERT: D 547 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8139 (tt) REVERT: C 56 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6789 (tptt) REVERT: C 112 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: E 56 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6553 (tptt) REVERT: E 140 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7606 (mtpm) REVERT: O 7 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6192 (mt0) REVERT: O 10 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7261 (m) REVERT: P 6 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: P 97 TYR cc_start: 0.8337 (m-80) cc_final: 0.8115 (m-80) outliers start: 83 outliers final: 44 residues processed: 247 average time/residue: 1.1518 time to fit residues: 309.9322 Evaluate side-chains 223 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 92 VAL 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 F 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 112 GLU Chi-restraints excluded: chain C residue 216 THR 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 135 CYS 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 7 GLN 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 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 117 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 514 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.183011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145434 restraints weight = 14009.007| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.27 r_work: 0.3303 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2372 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= 0.140 Angle : 0.630 6.635 16860 Z= 0.326 Chirality : 0.047 0.427 1833 Planarity : 0.004 0.042 2187 Dihedral : 7.015 59.694 1873 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.50 % Allowed : 17.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1536 helix: 1.63 (0.48), residues: 126 sheet: 0.64 (0.20), residues: 591 loop : -0.57 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 47 HIS 0.003 0.001 HIS U 37 PHE 0.012 0.002 PHE E 225 TYR 0.013 0.001 TYR L 34 ARG 0.009 0.000 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.02425 ( 3) link_NAG-ASN : angle 5.15701 ( 9) link_BETA1-4 : bond 0.00762 ( 3) link_BETA1-4 : angle 2.16130 ( 9) hydrogen bonds : bond 0.04638 ( 447) hydrogen bonds : angle 5.22977 ( 1242) SS BOND : bond 0.00270 ( 21) SS BOND : angle 1.09521 ( 42) covalent geometry : bond 0.00312 (12360) covalent geometry : angle 0.61572 (16800) *********************** 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 239 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 170 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: H 43 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (mptp) REVERT: A 140 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7500 (mtpp) REVERT: B 547 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8321 (tt) REVERT: F 596 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7297 (mmt90) REVERT: C 56 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6960 (tptt) REVERT: C 127 ASP cc_start: 0.8203 (t0) cc_final: 0.7975 (p0) REVERT: E 56 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6674 (tptt) REVERT: E 140 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7669 (mtpm) REVERT: O 7 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6249 (mt0) REVERT: O 100 ASP cc_start: 0.7437 (m-30) cc_final: 0.7184 (m-30) REVERT: P 6 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: P 97 TYR cc_start: 0.8336 (m-80) cc_final: 0.8112 (m-80) outliers start: 69 outliers final: 39 residues processed: 214 average time/residue: 1.1966 time to fit residues: 278.1841 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU 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 85 MET 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 90 SER 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 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 92 VAL 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 92 VAL 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 U residue 24 THR Chi-restraints excluded: chain U residue 108 THR 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 98 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 64 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 514 ASN D 516 HIS C 61 ASN E 61 ASN E 188 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.185149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149580 restraints weight = 13874.088| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.82 r_work: 0.3363 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12387 Z= 0.104 Angle : 0.567 6.638 16860 Z= 0.288 Chirality : 0.046 0.439 1833 Planarity : 0.004 0.039 2187 Dihedral : 6.452 56.637 1866 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.47 % Allowed : 18.42 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1536 helix: 1.56 (0.47), residues: 126 sheet: 0.71 (0.21), residues: 543 loop : -0.55 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS O 37 PHE 0.011 0.001 PHE E 225 TYR 0.008 0.001 TYR U 52 ARG 0.009 0.000 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01723 ( 3) link_NAG-ASN : angle 4.93338 ( 9) link_BETA1-4 : bond 0.00354 ( 3) link_BETA1-4 : angle 1.98262 ( 9) hydrogen bonds : bond 0.03719 ( 447) hydrogen bonds : angle 4.92495 ( 1242) SS BOND : bond 0.00203 ( 21) SS BOND : angle 1.01238 ( 42) covalent geometry : bond 0.00217 (12360) covalent geometry : angle 0.55211 (16800) *********************** 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 228 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8698 (p90) cc_final: 0.7561 (p90) REVERT: H 6 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: H 43 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7534 (mptp) REVERT: H 62 TYR cc_start: 0.7543 (m-80) cc_final: 0.7247 (m-80) REVERT: A 54 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.6127 (mpt180) REVERT: A 84 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8338 (mttm) REVERT: B 514 ASN cc_start: 0.8214 (m-40) cc_final: 0.7995 (m-40) REVERT: D 545 GLU cc_start: 0.7630 (mp0) cc_final: 0.6937 (mp0) REVERT: D 596 ARG cc_start: 0.7714 (mmt90) cc_final: 0.7434 (mmt90) REVERT: F 564 GLU cc_start: 0.8100 (tt0) cc_final: 0.7863 (mt-10) REVERT: C 54 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6268 (tpm170) REVERT: E 56 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6691 (tptt) REVERT: E 127 ASP cc_start: 0.8328 (t0) cc_final: 0.8037 (p0) REVERT: E 136 ARG cc_start: 0.8519 (mtp180) cc_final: 0.8269 (ttm-80) REVERT: E 140 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7672 (mtpm) REVERT: O 7 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.6161 (mt0) REVERT: O 10 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7423 (m) REVERT: P 6 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: Y 106 TYR cc_start: 0.8007 (m-10) cc_final: 0.7806 (m-80) outliers start: 56 outliers final: 28 residues processed: 211 average time/residue: 1.1903 time to fit residues: 274.4248 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 : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL 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 135 CYS 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 F 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 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 140 LYS 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 U residue 24 THR Chi-restraints excluded: chain P residue 6 GLU 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 66 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 81 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 73 optimal weight: 0.0370 chunk 129 optimal weight: 5.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 516 HIS C 61 ASN E 61 ASN ** P 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 = 0.4080 r_free = 0.4080 target = 0.187128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.152177 restraints weight = 13656.476| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.38 r_work: 0.3348 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12387 Z= 0.140 Angle : 0.599 6.834 16860 Z= 0.306 Chirality : 0.046 0.415 1833 Planarity : 0.004 0.041 2187 Dihedral : 6.233 46.360 1858 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.58 % Allowed : 17.94 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1536 helix: 1.54 (0.48), residues: 126 sheet: 0.70 (0.20), residues: 585 loop : -0.61 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 47 HIS 0.003 0.001 HIS L 37 PHE 0.013 0.002 PHE A 225 TYR 0.011 0.001 TYR U 52 ARG 0.011 0.000 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01938 ( 3) link_NAG-ASN : angle 4.63280 ( 9) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 2.23549 ( 9) hydrogen bonds : bond 0.04260 ( 447) hydrogen bonds : angle 4.89394 ( 1242) SS BOND : bond 0.00268 ( 21) SS BOND : angle 1.00182 ( 42) covalent geometry : bond 0.00327 (12360) covalent geometry : angle 0.58611 (16800) *********************** 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 231 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7682 (mptp) REVERT: H 62 TYR cc_start: 0.7696 (m-80) cc_final: 0.7486 (m-80) REVERT: A 54 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5871 (tpm170) REVERT: A 140 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7599 (mtpp) REVERT: B 514 ASN cc_start: 0.8293 (m-40) cc_final: 0.8067 (m-40) REVERT: B 564 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7947 (tt0) REVERT: D 545 GLU cc_start: 0.7738 (mp0) cc_final: 0.6894 (mp0) REVERT: D 547 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8352 (tt) REVERT: C 54 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6240 (tpm170) REVERT: E 136 ARG cc_start: 0.8537 (mtp180) cc_final: 0.8323 (ttm170) REVERT: E 140 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7601 (mtpm) REVERT: P 6 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: P 43 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7360 (mptm) outliers start: 70 outliers final: 46 residues processed: 202 average time/residue: 1.2269 time to fit residues: 269.4486 Evaluate side-chains 210 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 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 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 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 563 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F 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 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 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 P residue 6 GLU Chi-restraints excluded: chain P residue 43 LYS 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 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 15 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 overall best weight: 0.6832 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.189292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154755 restraints weight = 13880.293| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.33 r_work: 0.3403 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12387 Z= 0.104 Angle : 0.556 7.443 16860 Z= 0.281 Chirality : 0.046 0.439 1833 Planarity : 0.004 0.041 2187 Dihedral : 5.788 45.426 1851 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 20.49 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1536 helix: 1.62 (0.47), residues: 126 sheet: 0.68 (0.21), residues: 537 loop : -0.55 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS A 154 PHE 0.011 0.001 PHE E 225 TYR 0.008 0.001 TYR P 97 ARG 0.012 0.000 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01850 ( 3) link_NAG-ASN : angle 4.96849 ( 9) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 2.13751 ( 9) hydrogen bonds : bond 0.03572 ( 447) hydrogen bonds : angle 4.73104 ( 1242) SS BOND : bond 0.00204 ( 21) SS BOND : angle 0.90704 ( 42) covalent geometry : bond 0.00223 (12360) covalent geometry : angle 0.54072 (16800) *********************** 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 210 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7663 (mptp) REVERT: A 54 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5861 (tpm170) REVERT: B 514 ASN cc_start: 0.8323 (m-40) cc_final: 0.8078 (m-40) REVERT: D 596 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7518 (mmt90) REVERT: C 54 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6221 (tpm170) REVERT: E 140 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7574 (mtpm) REVERT: O 10 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (m) REVERT: O 100 ASP cc_start: 0.7663 (m-30) cc_final: 0.7332 (m-30) outliers start: 43 outliers final: 30 residues processed: 193 average time/residue: 1.2439 time to fit residues: 260.6835 Evaluate side-chains 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain H residue 43 LYS 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 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 60 THR 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 66 VAL 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 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 132 optimal weight: 0.0060 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.8100 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.178849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141033 restraints weight = 13987.668| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.91 r_work: 0.3245 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12387 Z= 0.225 Angle : 0.686 7.818 16860 Z= 0.351 Chirality : 0.049 0.388 1833 Planarity : 0.005 0.043 2187 Dihedral : 6.152 53.081 1848 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.02 % Allowed : 19.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1536 helix: 1.32 (0.48), residues: 126 sheet: 0.49 (0.20), residues: 591 loop : -0.83 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS L 37 PHE 0.015 0.002 PHE A 225 TYR 0.016 0.002 TYR H 62 ARG 0.011 0.001 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.02064 ( 3) link_NAG-ASN : angle 4.17990 ( 9) link_BETA1-4 : bond 0.00432 ( 3) link_BETA1-4 : angle 2.66652 ( 9) hydrogen bonds : bond 0.05234 ( 447) hydrogen bonds : angle 5.12613 ( 1242) SS BOND : bond 0.00271 ( 21) SS BOND : angle 1.12037 ( 42) covalent geometry : bond 0.00556 (12360) covalent geometry : angle 0.67507 (16800) *********************** 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 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7605 (mptp) REVERT: A 54 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5943 (tpm170) REVERT: A 140 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7627 (mtpm) REVERT: B 514 ASN cc_start: 0.8443 (m-40) cc_final: 0.8236 (m-40) REVERT: B 564 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7969 (tt0) REVERT: D 547 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8324 (tt) REVERT: D 564 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7920 (tt0) REVERT: C 54 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6220 (tpm170) REVERT: C 112 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: E 140 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7626 (mtpm) outliers start: 63 outliers final: 40 residues processed: 192 average time/residue: 1.2020 time to fit residues: 251.2792 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL 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 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 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 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F 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 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 140 LYS Chi-restraints excluded: chain E residue 175 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 91 optimal weight: 0.0170 chunk 69 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 C 228 ASN E 61 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.184728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147277 restraints weight = 13970.560| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.98 r_work: 0.3295 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12387 Z= 0.103 Angle : 0.563 8.092 16860 Z= 0.284 Chirality : 0.046 0.449 1833 Planarity : 0.004 0.044 2187 Dihedral : 5.675 48.276 1845 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.35 % Allowed : 21.45 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1536 helix: 1.60 (0.48), residues: 126 sheet: 0.66 (0.21), residues: 531 loop : -0.66 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 47 HIS 0.002 0.000 HIS C 154 PHE 0.010 0.001 PHE E 225 TYR 0.009 0.001 TYR U 52 ARG 0.014 0.000 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01935 ( 3) link_NAG-ASN : angle 5.11509 ( 9) link_BETA1-4 : bond 0.00450 ( 3) link_BETA1-4 : angle 2.12952 ( 9) hydrogen bonds : bond 0.03501 ( 447) hydrogen bonds : angle 4.74367 ( 1242) SS BOND : bond 0.00198 ( 21) SS BOND : angle 1.04068 ( 42) covalent geometry : bond 0.00214 (12360) covalent geometry : angle 0.54664 (16800) *********************** 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 211 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7544 (mptp) REVERT: A 54 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5958 (tpm170) REVERT: B 514 ASN cc_start: 0.8397 (m-40) cc_final: 0.8196 (m-40) REVERT: C 54 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6192 (tpm170) REVERT: E 140 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7543 (mtpm) REVERT: E 219 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7215 (mtp180) outliers start: 42 outliers final: 29 residues processed: 195 average time/residue: 1.1688 time to fit residues: 248.5250 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 97 ARG Chi-restraints excluded: chain H residue 43 LYS 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 135 CYS 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 F 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 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 E 61 ASN ** P 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 = 0.4024 r_free = 0.4024 target = 0.182420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143296 restraints weight = 13892.380| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.84 r_work: 0.3312 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12387 Z= 0.114 Angle : 0.573 7.544 16860 Z= 0.289 Chirality : 0.045 0.419 1833 Planarity : 0.004 0.045 2187 Dihedral : 5.653 48.738 1845 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.35 % Allowed : 22.17 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1536 helix: 1.62 (0.47), residues: 126 sheet: 0.68 (0.21), residues: 543 loop : -0.63 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 PHE 0.011 0.001 PHE E 225 TYR 0.008 0.001 TYR Y 97 ARG 0.011 0.000 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01829 ( 3) link_NAG-ASN : angle 4.78944 ( 9) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 2.26805 ( 9) hydrogen bonds : bond 0.03685 ( 447) hydrogen bonds : angle 4.68146 ( 1242) SS BOND : bond 0.00194 ( 21) SS BOND : angle 1.00672 ( 42) covalent geometry : bond 0.00256 (12360) covalent geometry : angle 0.55839 (16800) *********************** 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 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7563 (mptp) REVERT: A 54 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5980 (tpm170) REVERT: A 140 LYS cc_start: 0.8025 (tppt) cc_final: 0.7620 (mtpm) REVERT: B 514 ASN cc_start: 0.8385 (m-40) cc_final: 0.8182 (m-40) REVERT: C 54 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6199 (tpm170) REVERT: E 140 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7550 (mtpm) outliers start: 42 outliers final: 32 residues processed: 186 average time/residue: 1.1682 time to fit residues: 237.3376 Evaluate side-chains 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL 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 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 135 CYS 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 F 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 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 29 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 120 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN F 549 HIS C 61 ASN E 61 ASN ** P 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 = 0.3974 r_free = 0.3974 target = 0.178237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140631 restraints weight = 13973.775| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.12 r_work: 0.3236 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12387 Z= 0.183 Angle : 0.652 7.512 16860 Z= 0.332 Chirality : 0.048 0.399 1833 Planarity : 0.004 0.048 2187 Dihedral : 5.857 50.910 1845 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.11 % Allowed : 22.49 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1536 helix: 1.43 (0.48), residues: 126 sheet: 0.52 (0.20), residues: 597 loop : -0.80 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS L 37 PHE 0.013 0.002 PHE A 225 TYR 0.012 0.002 TYR U 52 ARG 0.011 0.000 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01927 ( 3) link_NAG-ASN : angle 4.39755 ( 9) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 2.55968 ( 9) hydrogen bonds : bond 0.04737 ( 447) hydrogen bonds : angle 4.94499 ( 1242) SS BOND : bond 0.00259 ( 21) SS BOND : angle 1.14077 ( 42) covalent geometry : bond 0.00444 (12360) covalent geometry : angle 0.63973 (16800) ********************** 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 187 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7558 (mptp) REVERT: A 140 LYS cc_start: 0.8012 (tppt) cc_final: 0.7621 (mtpm) REVERT: B 514 ASN cc_start: 0.8437 (m-40) cc_final: 0.8236 (m-40) REVERT: C 54 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6225 (tpm170) REVERT: E 140 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7602 (mtpm) outliers start: 39 outliers final: 35 residues processed: 172 average time/residue: 1.2178 time to fit residues: 228.3562 Evaluate side-chains 184 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL 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 52 VAL Chi-restraints excluded: chain A residue 54 ARG 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 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F 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 92 VAL 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 140 LYS Chi-restraints excluded: chain E residue 175 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 11 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 54 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.182487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144190 restraints weight = 13850.268| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.09 r_work: 0.3342 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12387 Z= 0.107 Angle : 0.573 7.598 16860 Z= 0.288 Chirality : 0.046 0.441 1833 Planarity : 0.004 0.045 2187 Dihedral : 5.657 56.460 1845 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.95 % Allowed : 22.97 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1536 helix: 1.63 (0.48), residues: 126 sheet: 0.67 (0.21), residues: 531 loop : -0.66 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.000 HIS C 154 PHE 0.011 0.001 PHE E 225 TYR 0.007 0.001 TYR Y 97 ARG 0.010 0.000 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01821 ( 3) link_NAG-ASN : angle 5.04850 ( 9) link_BETA1-4 : bond 0.00321 ( 3) link_BETA1-4 : angle 2.23736 ( 9) hydrogen bonds : bond 0.03547 ( 447) hydrogen bonds : angle 4.68834 ( 1242) SS BOND : bond 0.00195 ( 21) SS BOND : angle 1.05200 ( 42) covalent geometry : bond 0.00236 (12360) covalent geometry : angle 0.55700 (16800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7772.37 seconds wall clock time: 133 minutes 15.48 seconds (7995.48 seconds total)