Starting phenix.real_space_refine on Sat Oct 24 01:43:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8i_10123/10_2026/6s8i_10123.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7644 2.51 5 N 2076 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12066 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 109} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 1.90, per 1000 atoms: 0.16 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 D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.09 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=1.99 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 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 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 527.4 milliseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 12.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.034A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.625A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 4.033A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.626A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.602A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.619A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.820A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY H 16 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 43 through 46 removed outlier: 4.666A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AB3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.603A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AB6, first strand: chain 'F' and resid 580 through 581 removed outlier: 4.665A pdb=" N LEU E 35 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.754A pdb=" N GLU C 106 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.753A pdb=" N GLU E 106 " --> pdb=" O CYS E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.595A pdb=" N TRP O 38 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.593A pdb=" N TRP U 38 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'U' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'P' and resid 3 through 7 removed outlier: 5.893A pdb=" N GLY P 16 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 3 through 7 removed outlier: 5.892A pdb=" N GLY Y 16 " --> pdb=" O SER Y 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 60 through 62 removed outlier: 4.727A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.29 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: 6499 17.07 - 34.13: 524 34.13 - 51.20: 165 51.20 - 68.27: 30 68.27 - 85.34: 12 Dihedral angle restraints: 7230 sinusoidal: 2805 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 7227 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: 0.04 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 14.076 85.336 4365 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 8.13 % Allowed : 7.42 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1536 helix: -0.10 (0.40), residues: 144 sheet: 0.61 (0.20), residues: 573 loop : -0.69 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 54 TYR 0.027 0.003 TYR L 94 PHE 0.034 0.003 PHE Y 70 TRP 0.017 0.002 TRP H 47 HIS 0.008 0.002 HIS U 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (12360) covalent geometry : angle 0.95494 / 0.53 (16800) SS BOND : bond 0.01725 / 1.26 ( 21) SS BOND : angle 1.98840 / 1.44 ( 42) hydrogen bonds : bond 0.15555 / 10.56 ( 447) hydrogen bonds : angle 7.43894 / 5.13 ( 1242) link_BETA1-4 : bond 0.06517 / 3.27 ( 3) link_BETA1-4 : angle 20.03866 / 10.38 ( 9) link_NAG-ASN : bond 0.00086 / 0.04 ( 3) link_NAG-ASN : angle 2.43164 / 1.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 260 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: C 56 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7052 (tptt) REVERT: E 56 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6766 (tptt) REVERT: E 156 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8025 (mt-10) REVERT: P 6 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: P 97 TYR cc_start: 0.8407 (m-80) cc_final: 0.8193 (m-80) REVERT: Y 53 SER cc_start: 0.7716 (t) cc_final: 0.7446 (p) outliers start: 102 outliers final: 38 residues processed: 346 average time/residue: 0.4561 time to fit residues: 173.6994 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 GLN L 82 GLN H 39 GLN A 39 HIS A 61 ASN A 107 ASN A 188 GLN B 516 HIS C 39 HIS C 61 ASN C 107 ASN E 39 HIS E 61 ASN E 107 ASN O 40 GLN O 41 GLN O 82 GLN U 40 GLN U 82 GLN P 39 GLN Y 39 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142710 restraints weight = 13972.923| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.88 r_work: 0.3242 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12387 Z= 0.182 Angle : 0.730 7.596 16860 Z= 0.373 Chirality : 0.049 0.428 1833 Planarity : 0.005 0.038 2187 Dihedral : 7.588 58.060 1770 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.86 % Allowed : 15.87 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1536 helix: 1.52 (0.48), residues: 126 sheet: 1.08 (0.22), residues: 507 loop : -0.62 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 596 TYR 0.018 0.002 TYR U 52 PHE 0.016 0.002 PHE H 70 TRP 0.014 0.002 TRP Y 47 HIS 0.006 0.002 HIS U 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (12360) covalent geometry : angle 0.71440 / 0.37 (16800) SS BOND : bond 0.00300 / 0.19 ( 21) SS BOND : angle 1.46551 / 0.92 ( 42) hydrogen bonds : bond 0.05760 / 4.01 ( 447) hydrogen bonds : angle 5.67819 / 3.86 ( 1242) link_BETA1-4 : bond 0.00241 / 0.12 ( 3) link_BETA1-4 : angle 4.00057 / 2.15 ( 9) link_NAG-ASN : bond 0.01244 / 0.63 ( 3) link_NAG-ASN : angle 4.46720 / 2.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: H 43 LYS cc_start: 0.7659 (tppt) cc_final: 0.7400 (mptp) REVERT: A 140 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7479 (mtpp) REVERT: B 547 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8286 (tt) REVERT: C 56 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6895 (tptt) REVERT: C 219 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6746 (mtp180) REVERT: E 56 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6592 (tptt) REVERT: E 140 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7676 (mtpp) REVERT: O 7 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6242 (mt0) REVERT: O 10 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7249 (m) REVERT: P 6 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: P 97 TYR cc_start: 0.8381 (m-80) cc_final: 0.8161 (m-80) REVERT: Y 106 TYR cc_start: 0.8113 (m-80) cc_final: 0.7901 (m-10) outliers start: 86 outliers final: 43 residues processed: 249 average time/residue: 0.5082 time to fit residues: 137.7825 Evaluate side-chains 227 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 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: [68, 84, 123, 27, 0, 7, 95, 71, 107, 148, 59] chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN D 516 HIS C 61 ASN E 61 ASN O 41 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.179599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142271 restraints weight = 14133.042| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.99 r_work: 0.3238 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12387 Z= 0.177 Angle : 0.676 8.101 16860 Z= 0.350 Chirality : 0.047 0.376 1833 Planarity : 0.005 0.040 2187 Dihedral : 6.818 58.585 1746 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.30 % Allowed : 16.99 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1536 helix: 1.54 (0.49), residues: 126 sheet: 0.58 (0.20), residues: 591 loop : -0.73 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 596 TYR 0.016 0.002 TYR U 52 PHE 0.014 0.002 PHE E 225 TRP 0.015 0.002 TRP P 107 HIS 0.004 0.001 HIS U 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (12360) covalent geometry : angle 0.66529 / 0.35 (16800) SS BOND : bond 0.00196 / 0.12 ( 21) SS BOND : angle 1.19441 / 0.76 ( 42) hydrogen bonds : bond 0.05184 / 3.56 ( 447) hydrogen bonds : angle 5.38734 / 3.67 ( 1242) link_BETA1-4 : bond 0.00719 / 0.36 ( 3) link_BETA1-4 : angle 2.54499 / 1.29 ( 9) link_NAG-ASN : bond 0.02452 / 1.23 ( 3) link_NAG-ASN : angle 3.93257 / 2.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 171 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8829 (p90) cc_final: 0.7491 (p90) REVERT: H 6 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6797 (mt-10) REVERT: H 43 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7520 (mptp) REVERT: A 54 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.6072 (tpm170) REVERT: A 140 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7515 (mtpp) REVERT: B 547 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 54 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6357 (tpm170) REVERT: C 56 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7017 (tptp) REVERT: C 112 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 219 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6733 (mtp180) REVERT: E 56 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6774 (tptt) REVERT: E 140 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7651 (mtpp) REVERT: O 7 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: P 6 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: P 97 TYR cc_start: 0.8400 (m-80) cc_final: 0.8169 (m-80) outliers start: 79 outliers final: 45 residues processed: 226 average time/residue: 0.5266 time to fit residues: 129.7297 Evaluate side-chains 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN 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 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 P residue 117 SER Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [139, 132, 43, 82, 147, 34, 80, 108, 8, 60, 105] chunk 139 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 0.0570 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN O 41 GLN ** 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 = 0.4048 r_free = 0.4048 target = 0.184757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149396 restraints weight = 13980.836| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.82 r_work: 0.3371 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12387 Z= 0.106 Angle : 0.575 6.726 16860 Z= 0.294 Chirality : 0.045 0.397 1833 Planarity : 0.004 0.046 2187 Dihedral : 6.019 58.857 1741 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.63 % Allowed : 18.82 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1536 helix: 1.58 (0.48), residues: 126 sheet: 0.66 (0.21), residues: 537 loop : -0.68 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 596 TYR 0.009 0.001 TYR U 52 PHE 0.012 0.001 PHE A 225 TRP 0.008 0.001 TRP Y 47 HIS 0.002 0.001 HIS O 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (12360) covalent geometry : angle 0.56340 / 0.29 (16800) SS BOND : bond 0.00233 / 0.14 ( 21) SS BOND : angle 1.07006 / 0.68 ( 42) hydrogen bonds : bond 0.03828 / 2.64 ( 447) hydrogen bonds : angle 5.02850 / 3.43 ( 1242) link_BETA1-4 : bond 0.00569 / 0.29 ( 3) link_BETA1-4 : angle 2.20009 / 1.27 ( 9) link_NAG-ASN : bond 0.01778 / 0.89 ( 3) link_NAG-ASN : angle 4.17664 / 2.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7519 (mptp) REVERT: A 54 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6168 (mpt180) REVERT: A 140 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7451 (mtpp) REVERT: B 514 ASN cc_start: 0.8290 (m110) cc_final: 0.8050 (m-40) REVERT: D 545 GLU cc_start: 0.7665 (mp0) cc_final: 0.6933 (mp0) REVERT: C 54 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6230 (tpm170) REVERT: C 112 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: E 56 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6761 (tptt) REVERT: E 140 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7621 (mtpm) REVERT: O 7 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6227 (mt0) REVERT: O 10 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7367 (m) REVERT: P 6 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: Y 43 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7671 (mptp) outliers start: 58 outliers final: 29 residues processed: 205 average time/residue: 0.5723 time to fit residues: 127.1396 Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain 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 112 GLU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain 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 Y residue 43 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [69, 30, 130, 95, 64, 134, 68, 128, 39, 9, 114] chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 64 optimal weight: 0.0070 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146794 restraints weight = 13989.238| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.66 r_work: 0.3350 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12387 Z= 0.161 Angle : 0.636 11.140 16860 Z= 0.324 Chirality : 0.046 0.366 1833 Planarity : 0.004 0.041 2187 Dihedral : 5.684 52.230 1730 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.66 % Allowed : 18.18 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1536 helix: 1.56 (0.49), residues: 126 sheet: 0.56 (0.20), residues: 558 loop : -0.81 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.013 0.001 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.012 0.002 TRP H 47 HIS 0.004 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (12360) covalent geometry : angle 0.61945 / 0.32 (16800) SS BOND : bond 0.00257 / 0.17 ( 21) SS BOND : angle 1.13922 / 0.72 ( 42) hydrogen bonds : bond 0.04616 / 3.19 ( 447) hydrogen bonds : angle 5.04257 / 3.43 ( 1242) link_BETA1-4 : bond 0.00303 / 0.15 ( 3) link_BETA1-4 : angle 2.00429 / 1.01 ( 9) link_NAG-ASN : bond 0.01526 / 0.75 ( 3) link_NAG-ASN : angle 5.64029 / 3.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7499 (mmm160) REVERT: H 43 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7568 (mptp) REVERT: A 54 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5920 (tpm170) REVERT: A 140 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7577 (mtpm) REVERT: B 514 ASN cc_start: 0.8397 (m110) cc_final: 0.8149 (m-40) REVERT: D 596 ARG cc_start: 0.7779 (mmt90) cc_final: 0.7476 (mmt90) REVERT: C 54 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6237 (tpm170) REVERT: C 112 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: E 140 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7626 (mtpm) REVERT: O 7 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6320 (mt0) REVERT: P 6 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: P 97 TYR cc_start: 0.8392 (m-80) cc_final: 0.8142 (m-80) REVERT: Y 43 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7644 (mptp) outliers start: 71 outliers final: 50 residues processed: 205 average time/residue: 0.5436 time to fit residues: 121.2637 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 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 59 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 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: [58, 125, 102, 114, 147, 77, 88, 107, 6, 28, 53] chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 147 optimal weight: 0.0870 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 41 GLN A 61 ASN C 61 ASN C 228 ASN E 61 ASN U 41 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.185553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149200 restraints weight = 13897.435| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.99 r_work: 0.3344 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12387 Z= 0.102 Angle : 0.559 10.304 16860 Z= 0.283 Chirality : 0.044 0.391 1833 Planarity : 0.004 0.047 2187 Dihedral : 5.124 49.076 1726 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.91 % Allowed : 20.26 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1536 helix: 1.71 (0.48), residues: 126 sheet: 0.57 (0.21), residues: 537 loop : -0.67 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 596 TYR 0.008 0.001 TYR E 99 PHE 0.011 0.001 PHE E 225 TRP 0.008 0.001 TRP Y 47 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (12360) covalent geometry : angle 0.54085 / 0.28 (16800) SS BOND : bond 0.00291 / 0.15 ( 21) SS BOND : angle 0.97974 / 0.60 ( 42) hydrogen bonds : bond 0.03535 / 2.44 ( 447) hydrogen bonds : angle 4.78197 / 3.27 ( 1242) link_BETA1-4 : bond 0.00356 / 0.17 ( 3) link_BETA1-4 : angle 2.04478 / 1.12 ( 9) link_NAG-ASN : bond 0.01527 / 0.76 ( 3) link_NAG-ASN : angle 5.61729 / 3.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (mptp) REVERT: H 62 TYR cc_start: 0.7641 (m-80) cc_final: 0.7435 (m-80) REVERT: A 54 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5893 (tpm170) REVERT: B 514 ASN cc_start: 0.8362 (m110) cc_final: 0.8106 (m-40) REVERT: C 112 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: E 140 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7587 (mtpm) REVERT: E 219 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7149 (mtp180) REVERT: O 7 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6222 (mt0) REVERT: O 10 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7323 (m) REVERT: O 100 ASP cc_start: 0.7579 (m-30) cc_final: 0.7283 (m-30) outliers start: 49 outliers final: 34 residues processed: 202 average time/residue: 0.5400 time to fit residues: 118.6345 Evaluate side-chains 202 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 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 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain E residue 52 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 O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 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: [45, 78, 122, 82, 87, 127, 7, 27, 41, 18, 8] chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN P 54 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Y 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.181007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145526 restraints weight = 14026.961| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.66 r_work: 0.3377 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12387 Z= 0.159 Angle : 0.626 9.680 16860 Z= 0.316 Chirality : 0.046 0.361 1833 Planarity : 0.004 0.045 2187 Dihedral : 5.247 54.339 1722 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.18 % Allowed : 19.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1536 helix: 1.66 (0.48), residues: 126 sheet: 0.46 (0.20), residues: 558 loop : -0.78 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 596 TYR 0.012 0.001 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (12360) covalent geometry : angle 0.60521 / 0.31 (16800) SS BOND : bond 0.00240 / 0.16 ( 21) SS BOND : angle 1.07122 / 0.66 ( 42) hydrogen bonds : bond 0.04364 / 3.02 ( 447) hydrogen bonds : angle 4.88340 / 3.33 ( 1242) link_BETA1-4 : bond 0.00405 / 0.20 ( 3) link_BETA1-4 : angle 1.74850 / 0.89 ( 9) link_NAG-ASN : bond 0.01350 / 0.67 ( 3) link_NAG-ASN : angle 6.46088 / 3.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7466 (mmm160) REVERT: H 43 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (mptp) REVERT: A 54 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5958 (tpm170) REVERT: A 140 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7568 (mtpm) REVERT: B 514 ASN cc_start: 0.8427 (m110) cc_final: 0.8178 (m-40) REVERT: D 596 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7509 (mmt90) REVERT: C 112 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: E 140 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7661 (mtpp) REVERT: O 7 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6342 (mt0) REVERT: O 10 SER cc_start: 0.7602 (OUTLIER) cc_final: 0.7394 (m) REVERT: O 100 ASP cc_start: 0.7817 (m-30) cc_final: 0.7475 (m-30) REVERT: P 97 TYR cc_start: 0.8360 (m-80) cc_final: 0.8158 (m-80) outliers start: 65 outliers final: 50 residues processed: 195 average time/residue: 0.5388 time to fit residues: 114.3472 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 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 D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 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 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [138, 25, 123, 16, 73, 90, 83, 128, 91, 3, 108] chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.182028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145150 restraints weight = 13823.381| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.78 r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3157 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= 0.140 Angle : 0.608 9.888 16860 Z= 0.306 Chirality : 0.045 0.371 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.299 56.597 1722 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.26 % Allowed : 19.70 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1536 helix: 1.62 (0.48), residues: 126 sheet: 0.46 (0.20), residues: 552 loop : -0.79 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.011 0.001 TYR U 52 PHE 0.013 0.002 PHE A 225 TRP 0.012 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12360) covalent geometry : angle 0.58601 / 0.30 (16800) SS BOND : bond 0.00222 / 0.14 ( 21) SS BOND : angle 1.04444 / 0.64 ( 42) hydrogen bonds : bond 0.04178 / 2.88 ( 447) hydrogen bonds : angle 4.84372 / 3.31 ( 1242) link_BETA1-4 : bond 0.00290 / 0.14 ( 3) link_BETA1-4 : angle 1.87395 / 0.97 ( 9) link_NAG-ASN : bond 0.01520 / 0.75 ( 3) link_NAG-ASN : angle 6.53576 / 3.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (mptp) REVERT: A 54 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.6013 (tpm170) REVERT: A 140 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7618 (mtpm) REVERT: B 514 ASN cc_start: 0.8422 (m110) cc_final: 0.8189 (m-40) REVERT: B 547 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8310 (tt) REVERT: E 140 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7646 (mtpp) REVERT: E 219 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7292 (mtp180) REVERT: O 7 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.6247 (mt0) REVERT: O 100 ASP cc_start: 0.7896 (m-30) cc_final: 0.7549 (m-30) REVERT: P 97 TYR cc_start: 0.8296 (m-80) cc_final: 0.8030 (m-80) outliers start: 66 outliers final: 45 residues processed: 200 average time/residue: 0.5136 time to fit residues: 112.1898 Evaluate side-chains 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain P residue 46 GLU Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 98 CYS Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [94, 103, 52, 34, 63, 60, 137, 58, 25, 42, 99] chunk 94 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 228 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 = 0.4037 r_free = 0.4037 target = 0.183551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146483 restraints weight = 13839.342| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.74 r_work: 0.3303 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12387 Z= 0.111 Angle : 0.582 10.296 16860 Z= 0.290 Chirality : 0.044 0.381 1833 Planarity : 0.004 0.045 2187 Dihedral : 4.978 50.297 1719 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.83 % Allowed : 21.61 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1536 helix: 1.78 (0.49), residues: 126 sheet: 0.59 (0.21), residues: 531 loop : -0.71 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 596 TYR 0.009 0.001 TYR U 52 PHE 0.012 0.001 PHE A 225 TRP 0.010 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (12360) covalent geometry : angle 0.55842 / 0.28 (16800) SS BOND : bond 0.00198 / 0.13 ( 21) SS BOND : angle 1.03970 / 0.61 ( 42) hydrogen bonds : bond 0.03651 / 2.51 ( 447) hydrogen bonds : angle 4.69916 / 3.21 ( 1242) link_BETA1-4 : bond 0.00361 / 0.18 ( 3) link_BETA1-4 : angle 1.80531 / 0.96 ( 9) link_NAG-ASN : bond 0.01534 / 0.76 ( 3) link_NAG-ASN : angle 6.57018 / 3.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7525 (mptp) REVERT: H 62 TYR cc_start: 0.7630 (m-80) cc_final: 0.7414 (m-80) REVERT: B 514 ASN cc_start: 0.8397 (m110) cc_final: 0.8154 (m-40) REVERT: E 140 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (mtpm) REVERT: E 219 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7278 (mtp180) REVERT: O 7 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6227 (mt0) REVERT: O 100 ASP cc_start: 0.7838 (m-30) cc_final: 0.7517 (m-30) outliers start: 48 outliers final: 35 residues processed: 188 average time/residue: 0.5264 time to fit residues: 107.8725 Evaluate side-chains 191 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 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 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 54 ARG 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 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [137, 44, 144, 60, 98, 117, 52, 108, 11, 95, 62] chunk 137 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 98 optimal weight: 0.0070 chunk 117 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN E 62 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.180556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143061 restraints weight = 14087.198| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.85 r_work: 0.3295 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12387 Z= 0.127 Angle : 0.604 9.993 16860 Z= 0.302 Chirality : 0.045 0.369 1833 Planarity : 0.004 0.048 2187 Dihedral : 5.036 50.699 1719 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.67 % Allowed : 21.69 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1536 helix: 1.73 (0.49), residues: 126 sheet: 0.62 (0.20), residues: 546 loop : -0.74 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 596 TYR 0.008 0.001 TYR Y 97 PHE 0.013 0.001 PHE A 225 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12360) covalent geometry : angle 0.58141 / 0.30 (16800) SS BOND : bond 0.00264 / 0.15 ( 21) SS BOND : angle 1.18324 / 0.67 ( 42) hydrogen bonds : bond 0.03896 / 2.68 ( 447) hydrogen bonds : angle 4.70301 / 3.21 ( 1242) link_BETA1-4 : bond 0.00308 / 0.15 ( 3) link_BETA1-4 : angle 1.85738 / 0.98 ( 9) link_NAG-ASN : bond 0.01493 / 0.74 ( 3) link_NAG-ASN : angle 6.44204 / 3.38 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7576 (mptp) REVERT: H 62 TYR cc_start: 0.7639 (m-80) cc_final: 0.7420 (m-80) REVERT: A 54 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5981 (tpm170) REVERT: B 514 ASN cc_start: 0.8413 (m110) cc_final: 0.8178 (m-40) REVERT: E 140 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7614 (mtpm) REVERT: E 219 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7313 (mtp180) REVERT: O 7 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6266 (mt0) REVERT: Y 56 ASP cc_start: 0.7189 (m-30) cc_final: 0.6913 (m-30) outliers start: 46 outliers final: 38 residues processed: 180 average time/residue: 0.5422 time to fit residues: 106.2977 Evaluate side-chains 194 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 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 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D 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 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: [109, 23, 39, 24, 84, 80, 96, 148, 108, 140, 75] chunk 109 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4030 r_free = 0.4030 target = 0.182583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145357 restraints weight = 13835.276| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.69 r_work: 0.3298 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3313 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= 0.165 Angle : 0.642 9.821 16860 Z= 0.324 Chirality : 0.046 0.357 1833 Planarity : 0.004 0.047 2187 Dihedral : 5.230 52.819 1719 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.23 % Allowed : 21.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1536 helix: 1.60 (0.49), residues: 126 sheet: 0.51 (0.20), residues: 564 loop : -0.81 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.011 0.001 TYR U 52 PHE 0.013 0.002 PHE A 225 TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (12360) covalent geometry : angle 0.62113 / 0.32 (16800) SS BOND : bond 0.00250 / 0.16 ( 21) SS BOND : angle 1.23668 / 0.72 ( 42) hydrogen bonds : bond 0.04477 / 3.08 ( 447) hydrogen bonds : angle 4.84342 / 3.31 ( 1242) link_BETA1-4 : bond 0.00310 / 0.15 ( 3) link_BETA1-4 : angle 1.90783 / 0.99 ( 9) link_NAG-ASN : bond 0.01522 / 0.76 ( 3) link_NAG-ASN : angle 6.36210 / 3.34 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3551.93 seconds wall clock time: 61 minutes 19.27 seconds (3679.27 seconds total)