Starting phenix.real_space_refine on Fri Sep 11 22:09:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8i_10123/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.cif" model { file = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8i_10123/09_2026/6s8i_10123.map" } 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-2.2.1-6174/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: 2.74, per 1000 atoms: 0.23 Number of scatterers: 12066 At special positions: 0 Unit cell: (101.88, 98.484, 123.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2295 8.00 N 2076 7.00 C 7644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.00 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.09 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.99 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 597.4 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: 0.40 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: 2.06 Time building geometry restraints manager: 1.40 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: 1.500 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- 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 / 1.42 ( 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 : 0.455 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: 0.4827 time to fit residues: 183.5859 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 107 TRP Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 107 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 / 0.87 ( 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: 0.7658 (tppt) cc_final: 0.7398 (mptp) REVERT: A 140 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7479 (mtpp) REVERT: B 547 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8285 (tt) REVERT: C 56 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6894 (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: 0.6591 (tptt) REVERT: E 140 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7675 (mtpp) REVERT: O 7 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6241 (mt0) REVERT: O 10 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.7246 (m) REVERT: P 6 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: P 97 TYR cc_start: 0.8380 (m-80) cc_final: 0.8160 (m-80) REVERT: Y 106 TYR cc_start: 0.8114 (m-80) cc_final: 0.7900 (m-10) outliers start: 86 outliers final: 43 residues processed: 249 average time/residue: 0.5657 time to fit residues: 153.3618 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 : 0.539 ------------------------------------------------------------------------------- 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: 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: 0.5980 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: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN B 514 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.181073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144406 restraints weight = 14134.051| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.85 r_work: 0.3283 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12387 Z= 0.151 Angle : 0.647 8.252 16860 Z= 0.334 Chirality : 0.046 0.385 1833 Planarity : 0.005 0.040 2187 Dihedral : 6.651 59.120 1746 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.66 % Allowed : 17.46 % Favored : 76.87 % 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: 0.06 (0.20), residues: 1536 helix: 1.64 (0.48), residues: 126 sheet: 0.63 (0.20), residues: 591 loop : -0.65 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 596 TYR 0.014 0.001 TYR U 52 PHE 0.013 0.002 PHE E 225 TRP 0.013 0.001 TRP P 107 HIS 0.003 0.001 HIS U 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (12360) covalent geometry : angle 0.63522 / 0.33 (16800) SS BOND : bond 0.00229 / 0.16 ( 21) SS BOND : angle 1.23504 / 0.78 ( 42) hydrogen bonds : bond 0.04813 / 3.31 ( 447) hydrogen bonds : angle 5.29460 / 3.61 ( 1242) link_BETA1-4 : bond 0.00744 / 0.38 ( 3) link_BETA1-4 : angle 2.61288 / 1.35 ( 9) link_NAG-ASN : bond 0.02819 / 1.43 ( 3) link_NAG-ASN : angle 4.13829 / 2.51 ( 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 249 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 178 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 TYR cc_start: 0.8780 (p90) cc_final: 0.7500 (p90) REVERT: H 6 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: H 43 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7561 (mptp) REVERT: A 54 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.6059 (tpm170) REVERT: A 140 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7493 (mtpp) REVERT: C 54 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6345 (tpm170) REVERT: C 56 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7024 (tptp) REVERT: C 112 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: E 56 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6778 (tptt) REVERT: E 140 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7623 (mtpp) REVERT: O 7 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6308 (mt0) REVERT: O 100 ASP cc_start: 0.7577 (m-30) cc_final: 0.7285 (m-30) REVERT: P 6 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: P 97 TYR cc_start: 0.8399 (m-80) cc_final: 0.8166 (m-80) outliers start: 71 outliers final: 40 residues processed: 226 average time/residue: 0.5681 time to fit residues: 139.4466 Evaluate side-chains 214 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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 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 92 VAL 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 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 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: chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.179793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142652 restraints weight = 14025.101| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.82 r_work: 0.3282 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2664 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= 0.166 Angle : 0.645 6.690 16860 Z= 0.333 Chirality : 0.046 0.362 1833 Planarity : 0.004 0.042 2187 Dihedral : 6.342 59.603 1740 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.30 % Allowed : 17.38 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1536 helix: 1.46 (0.49), residues: 126 sheet: 0.52 (0.20), residues: 597 loop : -0.81 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 596 TYR 0.014 0.002 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (12360) covalent geometry : angle 0.63536 / 0.33 (16800) SS BOND : bond 0.00262 / 0.17 ( 21) SS BOND : angle 1.21729 / 0.77 ( 42) hydrogen bonds : bond 0.04803 / 3.31 ( 447) hydrogen bonds : angle 5.19749 / 3.54 ( 1242) link_BETA1-4 : bond 0.00290 / 0.14 ( 3) link_BETA1-4 : angle 2.33274 / 1.25 ( 9) link_NAG-ASN : bond 0.01829 / 0.92 ( 3) link_NAG-ASN : angle 3.70644 / 2.23 ( 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 246 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 167 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7705 (mmm160) REVERT: H 43 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7643 (mptp) REVERT: H 56 ASP cc_start: 0.7491 (m-30) cc_final: 0.7193 (m-30) REVERT: A 54 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6125 (mpt180) REVERT: A 140 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7606 (mtpp) REVERT: B 514 ASN cc_start: 0.8367 (m110) cc_final: 0.8136 (m-40) REVERT: B 547 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8340 (tt) REVERT: D 547 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8280 (tt) REVERT: C 54 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6237 (tpm170) REVERT: C 112 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: E 56 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6839 (tptt) REVERT: E 140 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (mtpm) REVERT: O 7 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6353 (mt0) REVERT: O 100 ASP cc_start: 0.7838 (m-30) cc_final: 0.7494 (m-30) REVERT: P 6 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: P 19 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7462 (mmm160) REVERT: P 97 TYR cc_start: 0.8445 (m-80) cc_final: 0.8207 (m-80) REVERT: Y 43 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7627 (mptp) outliers start: 79 outliers final: 48 residues processed: 216 average time/residue: 0.5965 time to fit residues: 139.7376 Evaluate side-chains 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 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 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 B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 ARG 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 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 U residue 75 SER Chi-restraints excluded: chain P residue 6 GLU Chi-restraints excluded: chain P residue 19 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 95 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN E 188 GLN Y 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.179522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144023 restraints weight = 14017.708| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.65 r_work: 0.3325 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12387 Z= 0.199 Angle : 0.671 7.188 16860 Z= 0.348 Chirality : 0.047 0.358 1833 Planarity : 0.005 0.044 2187 Dihedral : 6.125 56.820 1732 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 6.78 % Allowed : 17.46 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1536 helix: 1.36 (0.49), residues: 126 sheet: 0.41 (0.20), residues: 594 loop : -0.94 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.016 0.002 TYR U 52 PHE 0.015 0.002 PHE A 225 TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (12360) covalent geometry : angle 0.66164 / 0.35 (16800) SS BOND : bond 0.00273 / 0.17 ( 21) SS BOND : angle 1.18085 / 0.76 ( 42) hydrogen bonds : bond 0.05201 / 3.58 ( 447) hydrogen bonds : angle 5.24850 / 3.57 ( 1242) link_BETA1-4 : bond 0.00207 / 0.11 ( 3) link_BETA1-4 : angle 2.41600 / 1.24 ( 9) link_NAG-ASN : bond 0.01969 / 0.99 ( 3) link_NAG-ASN : angle 3.80090 / 2.30 ( 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 240 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 155 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: A 54 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5934 (tpm170) REVERT: A 140 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7583 (mtpm) REVERT: B 514 ASN cc_start: 0.8427 (m110) cc_final: 0.8192 (m-40) REVERT: B 547 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8284 (tp) REVERT: D 547 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 54 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6258 (tpm170) REVERT: C 112 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 140 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7664 (mtpp) REVERT: O 7 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6283 (mt0) REVERT: O 100 ASP cc_start: 0.7903 (m-30) cc_final: 0.7665 (m-30) REVERT: P 97 TYR cc_start: 0.8342 (m-80) cc_final: 0.8091 (m-80) outliers start: 85 outliers final: 61 residues processed: 210 average time/residue: 0.5264 time to fit residues: 120.5139 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 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 B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 564 GLU 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 77 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 112 VAL 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 60 THR Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 41 GLN A 61 ASN A 228 ASN C 61 ASN C 228 ASN E 61 ASN P 54 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139221 restraints weight = 13992.072| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.90 r_work: 0.3233 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12387 Z= 0.193 Angle : 0.661 7.570 16860 Z= 0.342 Chirality : 0.047 0.367 1833 Planarity : 0.005 0.046 2187 Dihedral : 5.818 57.599 1725 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 6.54 % Allowed : 18.26 % 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: -0.42 (0.20), residues: 1536 helix: 1.35 (0.50), residues: 126 sheet: 0.41 (0.20), residues: 588 loop : -1.07 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.015 0.002 TYR U 52 PHE 0.015 0.002 PHE A 225 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (12360) covalent geometry : angle 0.65089 / 0.34 (16800) SS BOND : bond 0.00262 / 0.16 ( 21) SS BOND : angle 1.22665 / 0.77 ( 42) hydrogen bonds : bond 0.05051 / 3.48 ( 447) hydrogen bonds : angle 5.20508 / 3.56 ( 1242) link_BETA1-4 : bond 0.00243 / 0.12 ( 3) link_BETA1-4 : angle 2.40311 / 1.24 ( 9) link_NAG-ASN : bond 0.01754 / 0.88 ( 3) link_NAG-ASN : angle 3.74472 / 2.27 ( 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 229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 147 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7496 (mptp) REVERT: A 54 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5973 (tpm170) REVERT: A 140 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7597 (mtpm) REVERT: B 547 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (tp) REVERT: D 547 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (tt) REVERT: C 112 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: O 7 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6261 (mt0) REVERT: O 52 TYR cc_start: 0.8876 (p90) cc_final: 0.7741 (p90) REVERT: P 19 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7519 (mmm160) REVERT: Y 105 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6768 (ttt90) outliers start: 82 outliers final: 58 residues processed: 203 average time/residue: 0.5433 time to fit residues: 120.0262 Evaluate side-chains 211 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 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 B residue 547 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain F residue 563 ASN Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL 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 129 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain O residue 7 GLN Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 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 105 ARG Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN U 41 GLN 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 = 0.182969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146339 restraints weight = 13957.590| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.61 r_work: 0.3302 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12387 Z= 0.111 Angle : 0.568 7.607 16860 Z= 0.291 Chirality : 0.044 0.399 1833 Planarity : 0.004 0.046 2187 Dihedral : 5.353 54.377 1725 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 21.37 % 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: -0.23 (0.20), residues: 1536 helix: 1.61 (0.49), residues: 126 sheet: 0.62 (0.21), residues: 525 loop : -0.92 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 596 TYR 0.011 0.001 TYR U 52 PHE 0.012 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 0.00242 / 0.11 (12360) covalent geometry : angle 0.55621 / 0.29 (16800) SS BOND : bond 0.00257 / 0.14 ( 21) SS BOND : angle 1.06428 / 0.64 ( 42) hydrogen bonds : bond 0.03754 / 2.59 ( 447) hydrogen bonds : angle 4.85277 / 3.32 ( 1242) link_BETA1-4 : bond 0.00352 / 0.17 ( 3) link_BETA1-4 : angle 2.20514 / 1.22 ( 9) link_NAG-ASN : bond 0.01557 / 0.77 ( 3) link_NAG-ASN : angle 4.09587 / 2.49 ( 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 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.6161 (mpt180) REVERT: E 140 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7543 (mtpm) REVERT: O 7 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6283 (mt0) outliers start: 43 outliers final: 26 residues processed: 196 average time/residue: 0.5834 time to fit residues: 124.3922 Evaluate side-chains 186 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER 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 B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain 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 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 66 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.183711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146517 restraints weight = 13844.782| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.77 r_work: 0.3292 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3308 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= 0.105 Angle : 0.572 11.647 16860 Z= 0.288 Chirality : 0.044 0.388 1833 Planarity : 0.004 0.044 2187 Dihedral : 5.095 53.032 1719 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.59 % Allowed : 21.77 % 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: -0.15 (0.20), residues: 1536 helix: 1.74 (0.49), residues: 126 sheet: 0.55 (0.21), residues: 531 loop : -0.80 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 596 TYR 0.008 0.001 TYR U 52 PHE 0.013 0.001 PHE A 225 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (12360) covalent geometry : angle 0.55248 / 0.28 (16800) SS BOND : bond 0.00194 / 0.12 ( 21) SS BOND : angle 1.07522 / 0.63 ( 42) hydrogen bonds : bond 0.03540 / 2.46 ( 447) hydrogen bonds : angle 4.71384 / 3.21 ( 1242) link_BETA1-4 : bond 0.00512 / 0.25 ( 3) link_BETA1-4 : angle 1.91899 / 1.06 ( 9) link_NAG-ASN : bond 0.01590 / 0.79 ( 3) link_NAG-ASN : angle 5.76105 / 2.96 ( 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 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (p) REVERT: E 140 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7620 (mtpm) REVERT: O 7 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6222 (mt0) REVERT: P 19 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7505 (mmm160) outliers start: 45 outliers final: 30 residues processed: 186 average time/residue: 0.5791 time to fit residues: 117.1093 Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain 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 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 P residue 19 ARG Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 94 optimal weight: 7.9990 chunk 103 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN B 549 HIS F 549 HIS C 61 ASN E 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.177772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139921 restraints weight = 13953.120| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.91 r_work: 0.3226 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12387 Z= 0.197 Angle : 0.662 9.708 16860 Z= 0.338 Chirality : 0.047 0.354 1833 Planarity : 0.005 0.046 2187 Dihedral : 5.436 56.211 1719 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.99 % Allowed : 21.53 % 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: -0.29 (0.20), residues: 1536 helix: 1.47 (0.49), residues: 126 sheet: 0.47 (0.20), residues: 588 loop : -0.97 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 596 TYR 0.012 0.002 TYR U 52 PHE 0.015 0.002 PHE A 225 TRP 0.013 0.002 TRP H 47 HIS 0.003 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (12360) covalent geometry : angle 0.64598 / 0.33 (16800) SS BOND : bond 0.00283 / 0.17 ( 21) SS BOND : angle 1.27768 / 0.77 ( 42) hydrogen bonds : bond 0.04833 / 3.32 ( 447) hydrogen bonds : angle 4.97906 / 3.39 ( 1242) link_BETA1-4 : bond 0.00163 / 0.08 ( 3) link_BETA1-4 : angle 2.22604 / 1.15 ( 9) link_NAG-ASN : bond 0.01532 / 0.76 ( 3) link_NAG-ASN : angle 5.32508 / 2.83 ( 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 197 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.6018 (tpm170) REVERT: E 140 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7671 (mtpp) REVERT: O 7 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6312 (mt0) REVERT: O 52 TYR cc_start: 0.8815 (p90) cc_final: 0.7682 (p90) outliers start: 50 outliers final: 35 residues processed: 178 average time/residue: 0.5941 time to fit residues: 114.9503 Evaluate side-chains 181 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain A residue 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 B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 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 P residue 56 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 114 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 71 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 98 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN C 61 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144721 restraints weight = 13891.586| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.56 r_work: 0.3252 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12387 Z= 0.175 Angle : 0.649 10.211 16860 Z= 0.330 Chirality : 0.046 0.370 1833 Planarity : 0.005 0.053 2187 Dihedral : 5.497 57.276 1719 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.43 % Allowed : 22.09 % 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: -0.43 (0.20), residues: 1536 helix: 1.46 (0.49), residues: 126 sheet: 0.38 (0.20), residues: 567 loop : -1.05 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 596 TYR 0.013 0.001 TYR U 52 PHE 0.014 0.002 PHE A 225 TRP 0.013 0.002 TRP H 47 HIS 0.003 0.001 HIS F 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (12360) covalent geometry : angle 0.63248 / 0.33 (16800) SS BOND : bond 0.00259 / 0.16 ( 21) SS BOND : angle 1.24648 / 0.75 ( 42) hydrogen bonds : bond 0.04651 / 3.20 ( 447) hydrogen bonds : angle 4.99076 / 3.41 ( 1242) link_BETA1-4 : bond 0.00256 / 0.12 ( 3) link_BETA1-4 : angle 2.13460 / 1.11 ( 9) link_NAG-ASN : bond 0.01581 / 0.79 ( 3) link_NAG-ASN : angle 5.43812 / 2.86 ( 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 192 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 62 TYR cc_start: 0.7685 (m-80) cc_final: 0.7482 (m-80) REVERT: A 54 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.6041 (tpm170) REVERT: A 140 LYS cc_start: 0.7999 (tppt) cc_final: 0.7616 (mtpm) REVERT: E 140 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7660 (mtpp) REVERT: O 7 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6283 (mt0) REVERT: O 52 TYR cc_start: 0.8823 (p90) cc_final: 0.7662 (p90) outliers start: 43 outliers final: 35 residues processed: 177 average time/residue: 0.5957 time to fit residues: 114.7621 Evaluate side-chains 186 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER 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 52 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain C residue 52 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 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 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 85 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 109 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 228 ASN C 61 ASN E 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138242 restraints weight = 14035.852| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.94 r_work: 0.3221 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12387 Z= 0.226 Angle : 0.706 9.767 16860 Z= 0.362 Chirality : 0.048 0.356 1833 Planarity : 0.005 0.046 2187 Dihedral : 5.751 59.728 1719 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.15 % Allowed : 21.45 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.48 (0.20), residues: 1536 helix: 1.33 (0.50), residues: 126 sheet: 0.41 (0.20), residues: 594 loop : -1.18 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 596 TYR 0.016 0.002 TYR U 52 PHE 0.015 0.002 PHE A 225 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS U 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (12360) covalent geometry : angle 0.69207 / 0.36 (16800) SS BOND : bond 0.00311 / 0.19 ( 21) SS BOND : angle 1.30174 / 0.80 ( 42) hydrogen bonds : bond 0.05335 / 3.67 ( 447) hydrogen bonds : angle 5.19918 / 3.55 ( 1242) link_BETA1-4 : bond 0.00160 / 0.08 ( 3) link_BETA1-4 : angle 2.25505 / 1.14 ( 9) link_NAG-ASN : bond 0.01631 / 0.81 ( 3) link_NAG-ASN : angle 5.26426 / 2.78 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.70 seconds wall clock time: 65 minutes 53.74 seconds (3953.74 seconds total)