Starting phenix.real_space_refine on Wed Jan 14 10:42:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ahl_15446/01_2026/8ahl_15446.map" } resolution = 4.1 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= 0.000 sd= 0.006 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 34 5.16 5 C 9078 2.51 5 N 2926 2.21 5 O 3006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15044 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 2, 'TRANS': 242} Chain: "B" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1828 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "C" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1203 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1264 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.21 Number of scatterers: 15044 At special positions: 0 Unit cell: (124.02, 545.37, 90.63, 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 34 16.00 O 3006 8.00 N 2926 7.00 C 9078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 795 " - pdb=" SG CYS E 868 " distance=2.03 Simple disulfide: pdb=" SG CYS F 795 " - pdb=" SG CYS F 868 " distance=2.06 Simple disulfide: pdb=" SG CYS K 795 " - pdb=" SG CYS K 868 " distance=2.03 Simple disulfide: pdb=" SG CYS L 795 " - pdb=" SG CYS L 868 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 484.9 milliseconds 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 78.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 removed outlier: 3.938A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 70 through 83 removed outlier: 4.468A pdb=" N ARG A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 277 Processing helix chain 'B' and resid 41 through 277 Proline residue: B 64 - end of helix Proline residue: B 72 - end of helix removed outlier: 3.987A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 446 removed outlier: 4.258A pdb=" N ARG C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 446 Processing helix chain 'E' and resid 859 through 863 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'G' and resid 40 through 193 Proline residue: G 64 - end of helix Proline residue: G 72 - end of helix removed outlier: 4.018A pdb=" N ALA G 92 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 193 Proline residue: H 64 - end of helix Proline residue: H 72 - end of helix removed outlier: 4.104A pdb=" N ALA H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 446 removed outlier: 3.687A pdb=" N GLY I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL I 353 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 355 " --> pdb=" O ALA I 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 446 Processing helix chain 'K' and resid 833 through 837 removed outlier: 3.581A pdb=" N LYS K 837 " --> pdb=" O ASP K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 859 through 863 Processing helix chain 'L' and resid 859 through 863 Processing sheet with id=AA1, first strand: chain 'E' and resid 791 through 793 removed outlier: 4.133A pdb=" N ASP E 845 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 830 through 832 removed outlier: 3.571A pdb=" N ASN E 831 " --> pdb=" O VAL E 823 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP E 809 " --> pdb=" O VAL E 821 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL E 823 " --> pdb=" O MET E 807 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET E 807 " --> pdb=" O VAL E 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 869 through 872 removed outlier: 3.773A pdb=" N ALA E 870 " --> pdb=" O TYR E 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.916A pdb=" N GLN F 5 " --> pdb=" O ALA F 796 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER F 794 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 820 through 824 removed outlier: 5.030A pdb=" N MET F 820 " --> pdb=" O ARG F 811 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG F 811 " --> pdb=" O MET F 820 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 822 " --> pdb=" O TRP F 809 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 842 through 845 Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.996A pdb=" N CYS K 795 " --> pdb=" O VAL K 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL K 851 " --> pdb=" O CYS K 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA K 864 " --> pdb=" O VAL K 884 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL K 884 " --> pdb=" O ALA K 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.863A pdb=" N THR L 850 " --> pdb=" O ASP L 845 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP L 845 " --> pdb=" O THR L 850 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 841 " --> pdb=" O GLN L 854 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 830 through 832 removed outlier: 6.570A pdb=" N TRP L 809 " --> pdb=" O VAL L 821 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL L 823 " --> pdb=" O MET L 807 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET L 807 " --> pdb=" O VAL L 823 " (cutoff:3.500A) 1522 hydrogen bonds defined for protein. 4500 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: 2.55 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5584 1.34 - 1.46: 2825 1.46 - 1.59: 6666 1.59 - 1.72: 0 1.72 - 1.84: 60 Bond restraints: 15135 Sorted by residual: bond pdb=" N ILE K 804 " pdb=" CA ILE K 804 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.05e+00 bond pdb=" N HIS I 350 " pdb=" CA HIS I 350 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.23e+00 bond pdb=" N ARG I 349 " pdb=" CA ARG I 349 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.22e+00 bond pdb=" N ASN K 805 " pdb=" CA ASN K 805 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.48e+00 bond pdb=" N GLN I 348 " pdb=" CA GLN I 348 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.14e+00 ... (remaining 15130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 19953 3.15 - 6.31: 356 6.31 - 9.46: 45 9.46 - 12.61: 6 12.61 - 15.77: 3 Bond angle restraints: 20363 Sorted by residual: angle pdb=" C TYR H 42 " pdb=" N GLU H 43 " pdb=" CA GLU H 43 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" N THR F 885 " pdb=" CA THR F 885 " pdb=" C THR F 885 " ideal model delta sigma weight residual 108.07 115.90 -7.83 1.38e+00 5.25e-01 3.22e+01 angle pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " ideal model delta sigma weight residual 114.10 103.55 10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" CA LEU J 434 " pdb=" CB LEU J 434 " pdb=" CG LEU J 434 " ideal model delta sigma weight residual 116.30 100.53 15.77 3.50e+00 8.16e-02 2.03e+01 angle pdb=" CA LEU C 308 " pdb=" CB LEU C 308 " pdb=" CG LEU C 308 " ideal model delta sigma weight residual 116.30 101.19 15.11 3.50e+00 8.16e-02 1.86e+01 ... (remaining 20358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8404 17.95 - 35.89: 910 35.89 - 53.84: 126 53.84 - 71.78: 39 71.78 - 89.73: 32 Dihedral angle restraints: 9511 sinusoidal: 3867 harmonic: 5644 Sorted by residual: dihedral pdb=" CB CYS F 795 " pdb=" SG CYS F 795 " pdb=" SG CYS F 868 " pdb=" CB CYS F 868 " ideal model delta sinusoidal sigma weight residual -86.00 -32.69 -53.31 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA ARG H 80 " pdb=" C ARG H 80 " pdb=" N ARG H 81 " pdb=" CA ARG H 81 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ASP L 802 " pdb=" C ASP L 802 " pdb=" N GLY L 803 " pdb=" CA GLY L 803 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 9508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1999 0.074 - 0.149: 284 0.149 - 0.223: 32 0.223 - 0.298: 5 0.298 - 0.372: 3 Chirality restraints: 2323 Sorted by residual: chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA GLU B 76 " pdb=" N GLU B 76 " pdb=" C GLU B 76 " pdb=" CB GLU B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE H 38 " pdb=" CA ILE H 38 " pdb=" CG1 ILE H 38 " pdb=" CG2 ILE H 38 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2320 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 813 " -0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO L 814 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO L 814 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO L 814 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 809 " -0.037 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP F 809 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP F 809 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP F 809 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP F 809 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 809 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 809 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 809 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 809 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 809 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 77 " 0.017 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE A 77 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 77 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 77 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 77 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 77 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 77 " 0.002 2.00e-02 2.50e+03 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 155 2.46 - 3.07: 11582 3.07 - 3.68: 26361 3.68 - 4.29: 33826 4.29 - 4.90: 52991 Nonbonded interactions: 124915 Sorted by model distance: nonbonded pdb=" CB ILE K 804 " pdb=" CE1 TYR K 872 " model vdw 1.845 3.770 nonbonded pdb=" O GLY K 803 " pdb=" CD1 TYR K 872 " model vdw 1.883 3.340 nonbonded pdb=" O ALA D 282 " pdb=" OG1 THR D 285 " model vdw 1.995 3.040 nonbonded pdb=" CB ILE K 804 " pdb=" CZ TYR K 872 " model vdw 2.082 3.690 nonbonded pdb=" O VAL K 12 " pdb=" N SER K 887 " model vdw 2.088 3.120 ... (remaining 124910 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 277) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'F' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'K' and (resid 1 through 8 or resid 791 through 887)) selection = chain 'L' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 39 through 193) } ncs_group { reference = 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 group one per residue 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: 19.330 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.110 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 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 : 0.006 0.072 15139 Z= 0.325 Angle : 1.036 15.768 20371 Z= 0.590 Chirality : 0.053 0.372 2323 Planarity : 0.005 0.085 2759 Dihedral : 15.629 89.730 5819 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 31.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.18), residues: 1917 helix: 1.42 (0.12), residues: 1449 sheet: -2.73 (0.38), residues: 151 loop : -1.82 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG D 267 TYR 0.034 0.003 TYR G 42 PHE 0.054 0.007 PHE A 77 TRP 0.048 0.005 TRP F 809 HIS 0.015 0.002 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00642 (15135) covalent geometry : angle 1.03395 (20363) SS BOND : bond 0.01597 ( 4) SS BOND : angle 3.52902 ( 8) hydrogen bonds : bond 0.10368 ( 1512) hydrogen bonds : angle 5.94366 ( 4500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 524 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.5721 (m-10) cc_final: 0.5216 (m-10) REVERT: A 152 GLN cc_start: 0.7495 (pp30) cc_final: 0.7266 (pp30) REVERT: A 175 VAL cc_start: 0.7376 (t) cc_final: 0.7085 (p) REVERT: A 226 ASP cc_start: 0.6159 (m-30) cc_final: 0.5885 (m-30) REVERT: A 230 LEU cc_start: 0.7657 (mt) cc_final: 0.7296 (mt) REVERT: A 240 GLN cc_start: 0.7640 (tt0) cc_final: 0.6963 (mt0) REVERT: A 264 ARG cc_start: 0.6208 (mmp80) cc_final: 0.5969 (mmt-90) REVERT: B 201 ARG cc_start: 0.6776 (ttt90) cc_final: 0.6492 (ttt90) REVERT: B 230 LEU cc_start: 0.7627 (mt) cc_final: 0.7424 (mt) REVERT: C 245 ARG cc_start: 0.6296 (ptt180) cc_final: 0.6054 (ptp90) REVERT: C 266 ILE cc_start: 0.7877 (mm) cc_final: 0.7636 (mm) REVERT: C 267 ARG cc_start: 0.7622 (mmp80) cc_final: 0.7220 (mmp80) REVERT: C 276 ASN cc_start: 0.7079 (m-40) cc_final: 0.6612 (m-40) REVERT: C 277 ARG cc_start: 0.6993 (tpm170) cc_final: 0.6409 (tpp80) REVERT: C 297 LEU cc_start: 0.8658 (tp) cc_final: 0.7479 (tp) REVERT: C 389 ARG cc_start: 0.6557 (ttp-110) cc_final: 0.6158 (ttm110) REVERT: C 396 GLN cc_start: 0.6274 (tm-30) cc_final: 0.5717 (tm-30) REVERT: C 404 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7535 (ptp90) REVERT: C 434 LEU cc_start: 0.7579 (tp) cc_final: 0.7368 (tp) REVERT: D 241 LEU cc_start: 0.6483 (mt) cc_final: 0.6214 (mt) REVERT: D 277 ARG cc_start: 0.8001 (tmt-80) cc_final: 0.7452 (tpt-90) REVERT: D 297 LEU cc_start: 0.8464 (mp) cc_final: 0.7902 (mt) REVERT: D 298 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6232 (mm-30) REVERT: D 420 ILE cc_start: 0.8219 (tp) cc_final: 0.7910 (tp) REVERT: D 445 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7195 (tm-30) REVERT: F 1 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5391 (tm-30) REVERT: G 115 LEU cc_start: 0.7607 (tp) cc_final: 0.6858 (tp) REVERT: G 156 LYS cc_start: 0.7711 (pptt) cc_final: 0.7412 (pptt) REVERT: H 115 LEU cc_start: 0.7251 (tp) cc_final: 0.6973 (tp) REVERT: H 131 THR cc_start: 0.7947 (p) cc_final: 0.7738 (p) REVERT: I 340 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5844 (mm-30) REVERT: I 363 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.7108 (tmm160) REVERT: I 395 MET cc_start: 0.7576 (tmm) cc_final: 0.7304 (tmm) REVERT: I 410 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6622 (mm-30) REVERT: I 422 ARG cc_start: 0.6539 (ttt90) cc_final: 0.5699 (tpp80) REVERT: I 442 SER cc_start: 0.7231 (t) cc_final: 0.7009 (t) REVERT: J 378 LEU cc_start: 0.6997 (tt) cc_final: 0.6465 (tp) REVERT: J 396 GLN cc_start: 0.7096 (pp30) cc_final: 0.6816 (pp30) REVERT: J 423 LEU cc_start: 0.7838 (mm) cc_final: 0.7347 (mt) REVERT: K 833 VAL cc_start: 0.7782 (t) cc_final: 0.7192 (t) REVERT: K 857 ASN cc_start: 0.7741 (p0) cc_final: 0.7493 (p0) REVERT: L 835 SER cc_start: 0.8479 (p) cc_final: 0.8113 (p) REVERT: L 861 GLU cc_start: 0.6548 (pp20) cc_final: 0.6054 (pp20) outliers start: 1 outliers final: 1 residues processed: 525 average time/residue: 0.1643 time to fit residues: 115.8086 Evaluate side-chains 478 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.0040 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.0970 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN A 276 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 272 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 100 GLN G 139 ASN G 173 HIS H 98 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN K 805 ASN K 817 GLN K 856 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.153169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.137858 restraints weight = 26084.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.142034 restraints weight = 12989.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.144607 restraints weight = 7217.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.146252 restraints weight = 4394.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.147277 restraints weight = 2895.198| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15139 Z= 0.187 Angle : 0.722 11.889 20371 Z= 0.388 Chirality : 0.043 0.208 2323 Planarity : 0.005 0.057 2759 Dihedral : 4.987 27.674 2184 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.66 % Allowed : 7.39 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.19), residues: 1917 helix: 2.35 (0.12), residues: 1422 sheet: -2.42 (0.38), residues: 146 loop : -1.43 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 41 TYR 0.033 0.002 TYR H 42 PHE 0.033 0.005 PHE A 77 TRP 0.023 0.003 TRP E 809 HIS 0.013 0.002 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00370 (15135) covalent geometry : angle 0.72039 (20363) SS BOND : bond 0.00729 ( 4) SS BOND : angle 2.43773 ( 8) hydrogen bonds : bond 0.05642 ( 1512) hydrogen bonds : angle 4.60038 ( 4500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 526 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6618 (m-10) cc_final: 0.5991 (m-10) REVERT: A 50 ASP cc_start: 0.6861 (m-30) cc_final: 0.6610 (m-30) REVERT: A 151 LEU cc_start: 0.8325 (mt) cc_final: 0.8072 (mt) REVERT: A 161 ASP cc_start: 0.6610 (t70) cc_final: 0.5726 (t70) REVERT: A 182 ARG cc_start: 0.5788 (mtm110) cc_final: 0.5551 (mtm110) REVERT: A 203 ASN cc_start: 0.8186 (m-40) cc_final: 0.7963 (m110) REVERT: A 230 LEU cc_start: 0.8268 (mt) cc_final: 0.7892 (mt) REVERT: A 234 GLU cc_start: 0.7169 (pp20) cc_final: 0.6390 (pp20) REVERT: A 236 ASP cc_start: 0.7727 (t0) cc_final: 0.7449 (t70) REVERT: A 237 LEU cc_start: 0.7847 (mm) cc_final: 0.7557 (mm) REVERT: A 272 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 62 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6239 (mp) REVERT: B 201 ARG cc_start: 0.7648 (ttt90) cc_final: 0.7421 (ttt90) REVERT: B 212 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 226 ASP cc_start: 0.7780 (m-30) cc_final: 0.7428 (m-30) REVERT: B 258 HIS cc_start: 0.5333 (m-70) cc_final: 0.4626 (m-70) REVERT: C 245 ARG cc_start: 0.7520 (ptt180) cc_final: 0.7205 (ptt-90) REVERT: C 258 HIS cc_start: 0.6925 (t-90) cc_final: 0.6720 (t-90) REVERT: C 266 ILE cc_start: 0.8338 (mm) cc_final: 0.8135 (mm) REVERT: C 276 ASN cc_start: 0.7696 (m-40) cc_final: 0.7285 (m-40) REVERT: C 277 ARG cc_start: 0.8234 (tpm170) cc_final: 0.7695 (tpp80) REVERT: C 280 ILE cc_start: 0.7483 (mm) cc_final: 0.7005 (mm) REVERT: C 286 ARG cc_start: 0.8071 (ptt-90) cc_final: 0.7731 (mtm110) REVERT: C 297 LEU cc_start: 0.8664 (tp) cc_final: 0.7918 (tp) REVERT: C 321 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7481 (tmm-80) REVERT: C 396 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6295 (tm-30) REVERT: D 219 ARG cc_start: 0.6331 (mmp80) cc_final: 0.6004 (mmp80) REVERT: D 220 VAL cc_start: 0.5658 (t) cc_final: 0.5403 (t) REVERT: D 277 ARG cc_start: 0.8276 (tmt-80) cc_final: 0.8003 (tpt-90) REVERT: D 283 LEU cc_start: 0.8051 (mm) cc_final: 0.7800 (mm) REVERT: D 286 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7633 (mtm180) REVERT: D 298 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6423 (mm-30) REVERT: D 299 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7104 (mm-30) REVERT: D 300 MET cc_start: 0.7070 (pmm) cc_final: 0.6858 (pmm) REVERT: D 416 LEU cc_start: 0.7640 (mp) cc_final: 0.7432 (mm) REVERT: D 420 ILE cc_start: 0.7625 (tp) cc_final: 0.7322 (tp) REVERT: D 429 LEU cc_start: 0.8431 (tp) cc_final: 0.8215 (tp) REVERT: D 438 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6717 (ttp80) REVERT: D 445 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6611 (tm-30) REVERT: E 3 GLN cc_start: 0.8314 (mm110) cc_final: 0.7617 (mm-40) REVERT: E 5 GLN cc_start: 0.7901 (mp-120) cc_final: 0.7667 (mm-40) REVERT: E 807 MET cc_start: 0.7366 (mmp) cc_final: 0.7105 (mmm) REVERT: E 882 THR cc_start: 0.8030 (t) cc_final: 0.7562 (p) REVERT: F 873 ARG cc_start: 0.7255 (mpt-90) cc_final: 0.6942 (mtt-85) REVERT: G 100 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7377 (pp30) REVERT: G 156 LYS cc_start: 0.8158 (pptt) cc_final: 0.7818 (pptt) REVERT: G 168 THR cc_start: 0.6964 (p) cc_final: 0.6196 (p) REVERT: G 173 HIS cc_start: 0.7881 (m90) cc_final: 0.7476 (m90) REVERT: H 43 GLU cc_start: 0.7255 (pm20) cc_final: 0.7000 (pm20) REVERT: H 56 MET cc_start: 0.8020 (mmp) cc_final: 0.7722 (mmp) REVERT: H 80 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6449 (ptm160) REVERT: H 114 ARG cc_start: 0.6939 (ttt-90) cc_final: 0.6503 (tmm-80) REVERT: H 128 ARG cc_start: 0.7099 (ptm160) cc_final: 0.6893 (ptm160) REVERT: H 133 ASP cc_start: 0.7958 (m-30) cc_final: 0.7688 (m-30) REVERT: H 160 LEU cc_start: 0.7924 (pp) cc_final: 0.7648 (pp) REVERT: I 339 LEU cc_start: 0.8795 (mt) cc_final: 0.8480 (mt) REVERT: I 363 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.7537 (tmm160) REVERT: I 395 MET cc_start: 0.7386 (tmm) cc_final: 0.7175 (tmm) REVERT: I 410 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7156 (mm-30) REVERT: I 415 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7184 (tm-30) REVERT: I 419 THR cc_start: 0.7701 (p) cc_final: 0.7445 (p) REVERT: I 426 GLU cc_start: 0.7099 (mp0) cc_final: 0.6523 (mp0) REVERT: I 434 LEU cc_start: 0.8014 (mm) cc_final: 0.7584 (mm) REVERT: I 435 GLU cc_start: 0.6056 (tp30) cc_final: 0.5489 (tp30) REVERT: I 438 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7361 (mtt90) REVERT: I 442 SER cc_start: 0.6622 (t) cc_final: 0.6294 (t) REVERT: J 375 GLU cc_start: 0.7220 (tp30) cc_final: 0.6885 (tp30) REVERT: J 378 LEU cc_start: 0.6805 (tt) cc_final: 0.6386 (tp) REVERT: J 383 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: J 388 LEU cc_start: 0.9009 (tt) cc_final: 0.8472 (tt) REVERT: J 421 GLU cc_start: 0.7190 (mp0) cc_final: 0.6266 (mp0) REVERT: J 426 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6910 (mt-10) REVERT: J 435 GLU cc_start: 0.6934 (tp30) cc_final: 0.6379 (tp30) REVERT: K 4 LEU cc_start: 0.7450 (mt) cc_final: 0.7165 (mt) REVERT: K 809 TRP cc_start: 0.7580 (m100) cc_final: 0.6988 (m100) REVERT: K 833 VAL cc_start: 0.8235 (t) cc_final: 0.6886 (t) REVERT: K 837 LYS cc_start: 0.8819 (mttp) cc_final: 0.8558 (mttm) REVERT: K 841 ILE cc_start: 0.7084 (mp) cc_final: 0.6780 (mp) REVERT: K 863 THR cc_start: 0.8705 (t) cc_final: 0.8298 (m) REVERT: L 801 ILE cc_start: 0.7502 (tp) cc_final: 0.7102 (tp) REVERT: L 839 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8477 (mtp85) outliers start: 10 outliers final: 4 residues processed: 531 average time/residue: 0.1579 time to fit residues: 113.7253 Evaluate side-chains 490 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 483 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 160 optimal weight: 0.6980 chunk 173 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 96 optimal weight: 0.2980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 259 GLN C 240 GLN C 249 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 249 GLN D 272 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS E 805 ASN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN I 350 HIS ** K 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 856 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.154861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.139471 restraints weight = 25742.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.143600 restraints weight = 13099.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.146196 restraints weight = 7423.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.147824 restraints weight = 4581.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.148911 restraints weight = 3067.986| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15139 Z= 0.212 Angle : 0.731 12.586 20371 Z= 0.396 Chirality : 0.044 0.226 2323 Planarity : 0.005 0.071 2759 Dihedral : 4.883 27.239 2184 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.26 % Allowed : 6.60 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.18), residues: 1917 helix: 2.51 (0.12), residues: 1426 sheet: -2.37 (0.36), residues: 171 loop : -1.42 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 219 TYR 0.019 0.002 TYR G 42 PHE 0.046 0.004 PHE A 77 TRP 0.020 0.003 TRP E 809 HIS 0.008 0.002 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00421 (15135) covalent geometry : angle 0.73006 (20363) SS BOND : bond 0.00872 ( 4) SS BOND : angle 2.34624 ( 8) hydrogen bonds : bond 0.05578 ( 1512) hydrogen bonds : angle 4.54100 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 524 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6804 (m-30) cc_final: 0.6589 (m-30) REVERT: A 151 LEU cc_start: 0.8339 (mt) cc_final: 0.8069 (mt) REVERT: A 230 LEU cc_start: 0.8372 (mt) cc_final: 0.8166 (mt) REVERT: A 233 ILE cc_start: 0.8007 (tp) cc_final: 0.7794 (tp) REVERT: A 236 ASP cc_start: 0.8043 (t0) cc_final: 0.7803 (t70) REVERT: A 237 LEU cc_start: 0.7855 (mm) cc_final: 0.7364 (mm) REVERT: B 80 ARG cc_start: 0.5843 (mtm-85) cc_final: 0.5006 (mtm-85) REVERT: B 107 GLU cc_start: 0.6986 (tt0) cc_final: 0.6654 (tm-30) REVERT: B 201 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7364 (ttt90) REVERT: B 212 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 219 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7513 (ttm170) REVERT: B 226 ASP cc_start: 0.7735 (m-30) cc_final: 0.7282 (m-30) REVERT: B 247 ARG cc_start: 0.8250 (mmp80) cc_final: 0.8026 (mmm160) REVERT: B 255 LEU cc_start: 0.7618 (tt) cc_final: 0.7299 (tt) REVERT: B 258 HIS cc_start: 0.5191 (m-70) cc_final: 0.4383 (m-70) REVERT: C 245 ARG cc_start: 0.7415 (ptt180) cc_final: 0.7198 (ptt180) REVERT: C 266 ILE cc_start: 0.8360 (mm) cc_final: 0.8127 (mm) REVERT: C 276 ASN cc_start: 0.7705 (m-40) cc_final: 0.7258 (m-40) REVERT: C 277 ARG cc_start: 0.8181 (tpm170) cc_final: 0.7582 (tpp80) REVERT: C 280 ILE cc_start: 0.7293 (mm) cc_final: 0.6759 (mm) REVERT: C 286 ARG cc_start: 0.8093 (ptt-90) cc_final: 0.7853 (mtm110) REVERT: C 295 ASP cc_start: 0.7738 (m-30) cc_final: 0.7321 (m-30) REVERT: C 297 LEU cc_start: 0.8645 (tp) cc_final: 0.8099 (tp) REVERT: C 396 GLN cc_start: 0.6838 (tm-30) cc_final: 0.6334 (tm-30) REVERT: C 423 LEU cc_start: 0.8090 (tp) cc_final: 0.7747 (tp) REVERT: D 219 ARG cc_start: 0.6289 (mmt-90) cc_final: 0.5871 (mmt180) REVERT: D 266 ILE cc_start: 0.8178 (mm) cc_final: 0.7584 (mm) REVERT: D 270 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6539 (mt-10) REVERT: D 272 GLN cc_start: 0.7524 (pt0) cc_final: 0.7137 (pt0) REVERT: D 276 ASN cc_start: 0.7996 (m-40) cc_final: 0.7325 (m-40) REVERT: D 286 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7462 (mtm180) REVERT: D 298 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6506 (mm-30) REVERT: D 299 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7145 (mm-30) REVERT: D 420 ILE cc_start: 0.7300 (tp) cc_final: 0.6956 (tp) REVERT: E 3 GLN cc_start: 0.8391 (mm110) cc_final: 0.7701 (mm-40) REVERT: G 115 LEU cc_start: 0.7563 (tp) cc_final: 0.7351 (tp) REVERT: G 156 LYS cc_start: 0.8234 (pptt) cc_final: 0.7716 (pptt) REVERT: G 173 HIS cc_start: 0.7833 (m90) cc_final: 0.7373 (m90) REVERT: H 43 GLU cc_start: 0.7212 (pm20) cc_final: 0.6975 (pm20) REVERT: H 93 ASN cc_start: 0.8441 (t0) cc_final: 0.8240 (t0) REVERT: H 114 ARG cc_start: 0.7092 (ttt-90) cc_final: 0.6716 (ttp80) REVERT: H 115 LEU cc_start: 0.7882 (tp) cc_final: 0.6753 (tp) REVERT: H 133 ASP cc_start: 0.7959 (m-30) cc_final: 0.7672 (m-30) REVERT: H 160 LEU cc_start: 0.8000 (pp) cc_final: 0.7602 (pp) REVERT: I 336 ILE cc_start: 0.8127 (mt) cc_final: 0.7410 (mt) REVERT: I 340 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6795 (mm-30) REVERT: I 341 GLU cc_start: 0.7391 (pt0) cc_final: 0.6956 (pt0) REVERT: I 395 MET cc_start: 0.7594 (tmm) cc_final: 0.7254 (tmm) REVERT: I 410 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7011 (mm-30) REVERT: I 415 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7482 (tm-30) REVERT: I 419 THR cc_start: 0.7692 (p) cc_final: 0.7453 (p) REVERT: I 435 GLU cc_start: 0.6010 (tp30) cc_final: 0.5545 (tp30) REVERT: I 438 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7265 (mtt90) REVERT: J 375 GLU cc_start: 0.7278 (tp30) cc_final: 0.6896 (tp30) REVERT: J 378 LEU cc_start: 0.6851 (tt) cc_final: 0.6468 (tp) REVERT: J 388 LEU cc_start: 0.8926 (tt) cc_final: 0.8485 (tt) REVERT: J 399 GLN cc_start: 0.8037 (tp40) cc_final: 0.7369 (tp40) REVERT: J 426 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6742 (mt-10) REVERT: J 435 GLU cc_start: 0.6914 (tp30) cc_final: 0.6498 (tp30) REVERT: J 446 MET cc_start: 0.3982 (tmm) cc_final: 0.3546 (mtt) REVERT: K 4 LEU cc_start: 0.7589 (mt) cc_final: 0.7364 (mt) REVERT: K 804 ILE cc_start: 0.7067 (tp) cc_final: 0.6485 (tp) REVERT: K 809 TRP cc_start: 0.7711 (m100) cc_final: 0.6732 (m100) REVERT: K 833 VAL cc_start: 0.8301 (t) cc_final: 0.7193 (t) REVERT: K 837 LYS cc_start: 0.8815 (mttp) cc_final: 0.8510 (mttp) REVERT: K 841 ILE cc_start: 0.6979 (mp) cc_final: 0.6696 (mp) REVERT: L 801 ILE cc_start: 0.7396 (tp) cc_final: 0.7076 (tp) REVERT: L 805 ASN cc_start: 0.8467 (t0) cc_final: 0.8181 (t0) REVERT: L 839 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8414 (mtp85) outliers start: 4 outliers final: 0 residues processed: 525 average time/residue: 0.1642 time to fit residues: 116.3900 Evaluate side-chains 482 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 99 optimal weight: 0.1980 chunk 161 optimal weight: 0.5980 chunk 138 optimal weight: 0.0980 chunk 65 optimal weight: 0.0980 chunk 126 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 139 optimal weight: 0.1980 chunk 178 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 108 optimal weight: 0.6980 overall best weight: 0.1298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 249 GLN D 272 GLN D 409 HIS ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 GLN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 856 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.158674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.142387 restraints weight = 25732.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.146877 restraints weight = 12703.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.149706 restraints weight = 7044.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.151479 restraints weight = 4261.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.152566 restraints weight = 2793.030| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15139 Z= 0.163 Angle : 0.684 10.496 20371 Z= 0.368 Chirality : 0.043 0.289 2323 Planarity : 0.004 0.049 2759 Dihedral : 4.643 25.908 2184 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.74 (0.19), residues: 1917 helix: 2.94 (0.12), residues: 1425 sheet: -2.10 (0.40), residues: 150 loop : -1.39 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 41 TYR 0.023 0.002 TYR K 810 PHE 0.040 0.006 PHE A 77 TRP 0.019 0.002 TRP F 809 HIS 0.012 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00319 (15135) covalent geometry : angle 0.68336 (20363) SS BOND : bond 0.00569 ( 4) SS BOND : angle 2.08471 ( 8) hydrogen bonds : bond 0.05363 ( 1512) hydrogen bonds : angle 4.24229 ( 4500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 545 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6640 (m-30) cc_final: 0.6228 (m-30) REVERT: A 151 LEU cc_start: 0.8296 (mt) cc_final: 0.8089 (mt) REVERT: A 161 ASP cc_start: 0.6815 (t70) cc_final: 0.6605 (t70) REVERT: A 203 ASN cc_start: 0.8075 (m110) cc_final: 0.7771 (p0) REVERT: A 230 LEU cc_start: 0.8389 (mt) cc_final: 0.8151 (mt) REVERT: A 232 ARG cc_start: 0.8625 (ttp80) cc_final: 0.8403 (ttp80) REVERT: A 233 ILE cc_start: 0.7975 (tp) cc_final: 0.7664 (tp) REVERT: A 236 ASP cc_start: 0.7845 (t0) cc_final: 0.7581 (t70) REVERT: A 237 LEU cc_start: 0.7955 (mm) cc_final: 0.7564 (mm) REVERT: A 238 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6195 (mt-10) REVERT: A 240 GLN cc_start: 0.7803 (tt0) cc_final: 0.7494 (tm-30) REVERT: A 264 ARG cc_start: 0.6526 (mmp80) cc_final: 0.6223 (mmp80) REVERT: B 80 ARG cc_start: 0.5445 (mtm-85) cc_final: 0.4838 (mtm-85) REVERT: B 125 SER cc_start: 0.7425 (t) cc_final: 0.7071 (m) REVERT: B 201 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7446 (ttt90) REVERT: B 212 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7324 (tp30) REVERT: B 226 ASP cc_start: 0.7826 (m-30) cc_final: 0.7318 (m-30) REVERT: B 247 ARG cc_start: 0.8280 (mmp80) cc_final: 0.7946 (mmm160) REVERT: B 255 LEU cc_start: 0.7664 (tt) cc_final: 0.7274 (tt) REVERT: B 258 HIS cc_start: 0.5394 (m-70) cc_final: 0.4784 (m-70) REVERT: C 245 ARG cc_start: 0.7484 (ptt180) cc_final: 0.7244 (ptt180) REVERT: C 258 HIS cc_start: 0.7002 (t-90) cc_final: 0.6793 (t-90) REVERT: C 266 ILE cc_start: 0.8354 (mm) cc_final: 0.7329 (mm) REVERT: C 267 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7883 (mmp80) REVERT: C 269 LEU cc_start: 0.7590 (mt) cc_final: 0.7264 (mt) REVERT: C 276 ASN cc_start: 0.7577 (m-40) cc_final: 0.7221 (m-40) REVERT: C 277 ARG cc_start: 0.8236 (tpm170) cc_final: 0.7831 (tpp80) REVERT: C 280 ILE cc_start: 0.7387 (mm) cc_final: 0.6996 (mm) REVERT: C 286 ARG cc_start: 0.8138 (ptt-90) cc_final: 0.7773 (mtm-85) REVERT: C 297 LEU cc_start: 0.8578 (tp) cc_final: 0.8161 (tp) REVERT: C 321 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7207 (tmm-80) REVERT: C 396 GLN cc_start: 0.6738 (tm-30) cc_final: 0.6188 (tm-30) REVERT: C 404 ARG cc_start: 0.8468 (ptt90) cc_final: 0.8092 (ptt90) REVERT: C 438 ARG cc_start: 0.6677 (mtm180) cc_final: 0.6399 (tmm-80) REVERT: D 219 ARG cc_start: 0.6407 (mmt-90) cc_final: 0.6097 (mmt180) REVERT: D 241 LEU cc_start: 0.7304 (mt) cc_final: 0.7020 (mt) REVERT: D 267 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7094 (ptt-90) REVERT: D 272 GLN cc_start: 0.7652 (pt0) cc_final: 0.7239 (pt0) REVERT: D 276 ASN cc_start: 0.7949 (m-40) cc_final: 0.7270 (m-40) REVERT: D 277 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7304 (tpt-90) REVERT: D 286 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7345 (mtm180) REVERT: D 298 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6551 (mm-30) REVERT: D 299 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 384 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7435 (ptm-80) REVERT: D 420 ILE cc_start: 0.7500 (tp) cc_final: 0.7199 (tp) REVERT: D 421 GLU cc_start: 0.8065 (tp30) cc_final: 0.7808 (tp30) REVERT: E 3 GLN cc_start: 0.8152 (mm110) cc_final: 0.7549 (mm-40) REVERT: E 4 LEU cc_start: 0.7580 (mp) cc_final: 0.7335 (mp) REVERT: F 859 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7137 (tmtt) REVERT: G 115 LEU cc_start: 0.7728 (tp) cc_final: 0.7179 (tp) REVERT: G 119 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6343 (mm-30) REVERT: G 139 ASN cc_start: 0.6398 (t0) cc_final: 0.6191 (t0) REVERT: G 156 LYS cc_start: 0.8111 (pptt) cc_final: 0.7758 (pptt) REVERT: G 173 HIS cc_start: 0.7868 (m90) cc_final: 0.7308 (m-70) REVERT: H 80 ARG cc_start: 0.7497 (ptm160) cc_final: 0.7276 (ptm160) REVERT: H 93 ASN cc_start: 0.7791 (t0) cc_final: 0.7516 (t0) REVERT: H 133 ASP cc_start: 0.8059 (m-30) cc_final: 0.7832 (m-30) REVERT: I 340 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6788 (mm-30) REVERT: I 341 GLU cc_start: 0.7517 (pt0) cc_final: 0.7099 (pt0) REVERT: I 395 MET cc_start: 0.7339 (tmm) cc_final: 0.7055 (tmm) REVERT: I 410 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7065 (mm-30) REVERT: I 412 LYS cc_start: 0.7523 (tptm) cc_final: 0.7227 (tptm) REVERT: I 415 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7508 (tm-30) REVERT: I 419 THR cc_start: 0.7723 (p) cc_final: 0.7379 (p) REVERT: I 421 GLU cc_start: 0.7710 (tp30) cc_final: 0.7460 (tp30) REVERT: I 435 GLU cc_start: 0.5850 (tp30) cc_final: 0.5331 (tp30) REVERT: J 375 GLU cc_start: 0.7188 (tp30) cc_final: 0.6840 (tp30) REVERT: J 378 LEU cc_start: 0.6785 (tt) cc_final: 0.6529 (tp) REVERT: J 388 LEU cc_start: 0.8879 (tt) cc_final: 0.8476 (tt) REVERT: J 426 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6725 (mt-10) REVERT: J 431 GLU cc_start: 0.7790 (tp30) cc_final: 0.7207 (tm-30) REVERT: J 435 GLU cc_start: 0.6920 (tp30) cc_final: 0.6422 (tp30) REVERT: J 446 MET cc_start: 0.3910 (tmm) cc_final: 0.3473 (mtt) REVERT: K 4 LEU cc_start: 0.7609 (mt) cc_final: 0.7354 (mt) REVERT: K 789 ASP cc_start: 0.6798 (p0) cc_final: 0.6597 (p0) REVERT: K 804 ILE cc_start: 0.7055 (tp) cc_final: 0.6465 (tp) REVERT: K 807 MET cc_start: 0.6872 (mmm) cc_final: 0.6513 (mmm) REVERT: K 809 TRP cc_start: 0.7536 (m100) cc_final: 0.6583 (m100) REVERT: K 833 VAL cc_start: 0.8255 (t) cc_final: 0.6886 (t) REVERT: K 837 LYS cc_start: 0.8878 (mttp) cc_final: 0.8495 (mttp) REVERT: K 859 LYS cc_start: 0.8150 (pttm) cc_final: 0.7930 (pttm) REVERT: L 4 LEU cc_start: 0.7599 (mp) cc_final: 0.7397 (mp) REVERT: L 805 ASN cc_start: 0.8182 (t0) cc_final: 0.7317 (t0) REVERT: L 807 MET cc_start: 0.7803 (pmm) cc_final: 0.7570 (pmm) REVERT: L 839 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8424 (mtp85) outliers start: 5 outliers final: 2 residues processed: 547 average time/residue: 0.1569 time to fit residues: 115.5554 Evaluate side-chains 482 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 172 optimal weight: 0.0870 chunk 143 optimal weight: 0.2980 chunk 102 optimal weight: 0.0970 chunk 125 optimal weight: 0.5980 chunk 176 optimal weight: 0.4980 chunk 87 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 0.0020 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 117 optimal weight: 0.9990 overall best weight: 0.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 249 GLN D 409 HIS E 805 ASN E 854 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 HIS K 817 GLN K 856 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.163657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.148560 restraints weight = 25926.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.153023 restraints weight = 12394.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.155732 restraints weight = 6612.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.157491 restraints weight = 3876.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.158553 restraints weight = 2441.852| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15139 Z= 0.160 Angle : 0.680 9.531 20371 Z= 0.364 Chirality : 0.042 0.238 2323 Planarity : 0.004 0.058 2759 Dihedral : 4.492 24.442 2184 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.01 (0.19), residues: 1917 helix: 3.12 (0.12), residues: 1434 sheet: -1.91 (0.41), residues: 150 loop : -1.45 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 384 TYR 0.024 0.002 TYR K 810 PHE 0.052 0.005 PHE A 77 TRP 0.030 0.002 TRP E 827 HIS 0.008 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00313 (15135) covalent geometry : angle 0.67965 (20363) SS BOND : bond 0.00365 ( 4) SS BOND : angle 1.42271 ( 8) hydrogen bonds : bond 0.05268 ( 1512) hydrogen bonds : angle 4.18162 ( 4500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6402 (m-30) cc_final: 0.5634 (m-30) REVERT: A 151 LEU cc_start: 0.8295 (mt) cc_final: 0.8025 (mt) REVERT: A 161 ASP cc_start: 0.6802 (t70) cc_final: 0.6200 (t70) REVERT: A 203 ASN cc_start: 0.8091 (m110) cc_final: 0.7573 (m110) REVERT: A 230 LEU cc_start: 0.8379 (mt) cc_final: 0.8174 (mt) REVERT: A 234 GLU cc_start: 0.7338 (pp20) cc_final: 0.7098 (pp20) REVERT: A 236 ASP cc_start: 0.8108 (t0) cc_final: 0.7823 (t70) REVERT: A 240 GLN cc_start: 0.7846 (tt0) cc_final: 0.7583 (tm-30) REVERT: B 80 ARG cc_start: 0.5422 (mtm-85) cc_final: 0.4658 (mtm-85) REVERT: B 226 ASP cc_start: 0.7806 (m-30) cc_final: 0.7240 (m-30) REVERT: B 255 LEU cc_start: 0.7722 (tt) cc_final: 0.7456 (tt) REVERT: B 258 HIS cc_start: 0.5343 (m-70) cc_final: 0.4871 (m-70) REVERT: C 245 ARG cc_start: 0.7521 (ptt180) cc_final: 0.7189 (ptt180) REVERT: C 258 HIS cc_start: 0.7022 (t-90) cc_final: 0.6777 (t-90) REVERT: C 265 THR cc_start: 0.8093 (p) cc_final: 0.7751 (p) REVERT: C 266 ILE cc_start: 0.8301 (mm) cc_final: 0.7682 (tp) REVERT: C 269 LEU cc_start: 0.7732 (mt) cc_final: 0.7418 (mt) REVERT: C 273 VAL cc_start: 0.7368 (t) cc_final: 0.7109 (t) REVERT: C 276 ASN cc_start: 0.7583 (m-40) cc_final: 0.7238 (m-40) REVERT: C 277 ARG cc_start: 0.8284 (tpm170) cc_final: 0.7770 (tpp80) REVERT: C 286 ARG cc_start: 0.8141 (ptt-90) cc_final: 0.7863 (mtm110) REVERT: C 297 LEU cc_start: 0.8518 (tp) cc_final: 0.8146 (tp) REVERT: C 321 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7213 (tmm-80) REVERT: C 396 GLN cc_start: 0.6682 (tm-30) cc_final: 0.6227 (tm-30) REVERT: C 438 ARG cc_start: 0.6571 (mtm180) cc_final: 0.6291 (ttm170) REVERT: D 219 ARG cc_start: 0.6075 (mmt-90) cc_final: 0.5871 (mmt180) REVERT: D 267 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7306 (ptp-170) REVERT: D 270 GLU cc_start: 0.6307 (pt0) cc_final: 0.6084 (pt0) REVERT: D 272 GLN cc_start: 0.8051 (tt0) cc_final: 0.7117 (tm-30) REVERT: D 276 ASN cc_start: 0.7865 (m-40) cc_final: 0.5783 (m-40) REVERT: D 285 THR cc_start: 0.8398 (p) cc_final: 0.7664 (p) REVERT: D 286 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7499 (mtm180) REVERT: D 298 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6583 (mm-30) REVERT: D 299 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7233 (mm-30) REVERT: D 318 VAL cc_start: 0.7672 (t) cc_final: 0.7418 (m) REVERT: D 412 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7330 (ttmm) REVERT: D 420 ILE cc_start: 0.7184 (tp) cc_final: 0.6899 (tp) REVERT: D 421 GLU cc_start: 0.8064 (tp30) cc_final: 0.7837 (tp30) REVERT: E 3 GLN cc_start: 0.8168 (mm110) cc_final: 0.7558 (mm-40) REVERT: E 827 TRP cc_start: 0.5431 (p-90) cc_final: 0.5077 (p-90) REVERT: E 882 THR cc_start: 0.7980 (t) cc_final: 0.7437 (p) REVERT: F 859 LYS cc_start: 0.7560 (tptp) cc_final: 0.7013 (tptp) REVERT: G 99 ARG cc_start: 0.7770 (ptp90) cc_final: 0.7523 (ptp-170) REVERT: G 115 LEU cc_start: 0.7784 (tp) cc_final: 0.6358 (tp) REVERT: G 119 GLU cc_start: 0.6830 (mm-30) cc_final: 0.5877 (mm-30) REVERT: G 156 LYS cc_start: 0.8129 (pptt) cc_final: 0.7711 (pptt) REVERT: G 173 HIS cc_start: 0.7888 (m90) cc_final: 0.7296 (m-70) REVERT: H 42 TYR cc_start: 0.6184 (m-80) cc_final: 0.5540 (m-80) REVERT: H 43 GLU cc_start: 0.7208 (mp0) cc_final: 0.6541 (pm20) REVERT: H 80 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7184 (ptm160) REVERT: H 94 LEU cc_start: 0.8201 (tp) cc_final: 0.7713 (tp) REVERT: H 114 ARG cc_start: 0.7387 (ttt-90) cc_final: 0.6710 (tmm-80) REVERT: H 115 LEU cc_start: 0.7904 (tp) cc_final: 0.6902 (tp) REVERT: I 336 ILE cc_start: 0.8028 (mt) cc_final: 0.7397 (mt) REVERT: I 340 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6844 (mm-30) REVERT: I 341 GLU cc_start: 0.7538 (pt0) cc_final: 0.7137 (pt0) REVERT: I 395 MET cc_start: 0.7251 (tmm) cc_final: 0.6898 (tmm) REVERT: I 410 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7089 (mm-30) REVERT: I 412 LYS cc_start: 0.7471 (tptm) cc_final: 0.7180 (tptm) REVERT: I 415 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7429 (tm-30) REVERT: I 419 THR cc_start: 0.7581 (p) cc_final: 0.7329 (p) REVERT: I 421 GLU cc_start: 0.7716 (tp30) cc_final: 0.7411 (tp30) REVERT: I 422 ARG cc_start: 0.7757 (tpt-90) cc_final: 0.6878 (tpp80) REVERT: I 426 GLU cc_start: 0.7010 (mp0) cc_final: 0.5425 (mp0) REVERT: I 435 GLU cc_start: 0.5676 (tp30) cc_final: 0.5455 (tp30) REVERT: J 375 GLU cc_start: 0.7375 (tp30) cc_final: 0.6953 (tp30) REVERT: J 388 LEU cc_start: 0.8843 (tt) cc_final: 0.8479 (tt) REVERT: J 423 LEU cc_start: 0.7922 (tp) cc_final: 0.7302 (tt) REVERT: J 426 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6683 (mt-10) REVERT: J 431 GLU cc_start: 0.7766 (tp30) cc_final: 0.7140 (tm-30) REVERT: J 435 GLU cc_start: 0.6990 (tp30) cc_final: 0.6356 (tp30) REVERT: J 446 MET cc_start: 0.3651 (tmm) cc_final: 0.3178 (mtt) REVERT: K 804 ILE cc_start: 0.7018 (tp) cc_final: 0.4961 (tp) REVERT: K 809 TRP cc_start: 0.7615 (m100) cc_final: 0.6751 (m100) REVERT: K 833 VAL cc_start: 0.8256 (t) cc_final: 0.6929 (t) REVERT: K 865 VAL cc_start: 0.8027 (t) cc_final: 0.7735 (p) REVERT: L 807 MET cc_start: 0.7867 (pmm) cc_final: 0.7629 (pmm) REVERT: L 824 VAL cc_start: 0.8224 (m) cc_final: 0.8018 (m) REVERT: L 839 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8451 (mtp85) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.1604 time to fit residues: 114.4024 Evaluate side-chains 473 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 116 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 183 optimal weight: 0.0980 chunk 53 optimal weight: 0.2980 chunk 179 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 104 optimal weight: 0.0870 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 249 GLN D 409 HIS ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN K 817 GLN K 856 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.148129 restraints weight = 25781.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.152548 restraints weight = 12466.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.155313 restraints weight = 6763.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.157051 restraints weight = 3972.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.158116 restraints weight = 2537.731| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15139 Z= 0.170 Angle : 0.695 10.116 20371 Z= 0.375 Chirality : 0.043 0.218 2323 Planarity : 0.005 0.088 2759 Dihedral : 4.537 25.260 2184 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.19), residues: 1917 helix: 3.07 (0.12), residues: 1432 sheet: -1.85 (0.42), residues: 141 loop : -1.48 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 129 TYR 0.023 0.002 TYR K 810 PHE 0.039 0.006 PHE A 77 TRP 0.022 0.002 TRP E 827 HIS 0.008 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00341 (15135) covalent geometry : angle 0.69430 (20363) SS BOND : bond 0.00491 ( 4) SS BOND : angle 1.70707 ( 8) hydrogen bonds : bond 0.05280 ( 1512) hydrogen bonds : angle 4.18984 ( 4500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6386 (m-30) cc_final: 0.6121 (m-30) REVERT: A 151 LEU cc_start: 0.8363 (mt) cc_final: 0.8106 (mt) REVERT: A 161 ASP cc_start: 0.6689 (t70) cc_final: 0.5014 (t70) REVERT: A 163 SER cc_start: 0.7739 (t) cc_final: 0.7339 (m) REVERT: A 203 ASN cc_start: 0.8047 (m110) cc_final: 0.7606 (m110) REVERT: A 232 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8355 (ttp80) REVERT: A 233 ILE cc_start: 0.7907 (tp) cc_final: 0.7692 (tp) REVERT: A 240 GLN cc_start: 0.7890 (tt0) cc_final: 0.7643 (tm-30) REVERT: A 264 ARG cc_start: 0.6352 (mmt180) cc_final: 0.6070 (mmp80) REVERT: B 80 ARG cc_start: 0.5150 (mtm-85) cc_final: 0.4385 (mtm-85) REVERT: B 226 ASP cc_start: 0.7818 (m-30) cc_final: 0.7306 (m-30) REVERT: B 247 ARG cc_start: 0.8285 (mmp80) cc_final: 0.7443 (mmm160) REVERT: B 255 LEU cc_start: 0.7621 (tt) cc_final: 0.7313 (tt) REVERT: B 258 HIS cc_start: 0.5259 (m-70) cc_final: 0.4791 (m-70) REVERT: C 245 ARG cc_start: 0.7552 (ptt180) cc_final: 0.7190 (ptt180) REVERT: C 258 HIS cc_start: 0.7008 (t-90) cc_final: 0.6748 (t-90) REVERT: C 267 ARG cc_start: 0.8028 (mmp80) cc_final: 0.7818 (mmp80) REVERT: C 276 ASN cc_start: 0.7515 (m-40) cc_final: 0.7141 (m-40) REVERT: C 277 ARG cc_start: 0.8284 (tpm170) cc_final: 0.7828 (tpp80) REVERT: C 280 ILE cc_start: 0.7335 (mm) cc_final: 0.7062 (mm) REVERT: C 286 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7824 (mtm180) REVERT: C 297 LEU cc_start: 0.8483 (tp) cc_final: 0.8120 (tp) REVERT: C 318 VAL cc_start: 0.7230 (t) cc_final: 0.6889 (t) REVERT: C 321 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7425 (ttp80) REVERT: C 396 GLN cc_start: 0.6725 (tm-30) cc_final: 0.6140 (tm-30) REVERT: C 404 ARG cc_start: 0.8469 (ptt90) cc_final: 0.7925 (ptp90) REVERT: C 410 GLU cc_start: 0.7776 (tp30) cc_final: 0.7228 (tp30) REVERT: D 219 ARG cc_start: 0.5631 (mmt-90) cc_final: 0.5385 (mmt180) REVERT: D 269 LEU cc_start: 0.7959 (tp) cc_final: 0.7708 (tp) REVERT: D 272 GLN cc_start: 0.8196 (tt0) cc_final: 0.7436 (mt0) REVERT: D 276 ASN cc_start: 0.7783 (m-40) cc_final: 0.7277 (m-40) REVERT: D 277 ARG cc_start: 0.8043 (tpt-90) cc_final: 0.7744 (tpt-90) REVERT: D 286 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7274 (mtm180) REVERT: D 298 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6613 (mm-30) REVERT: D 299 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7214 (mm-30) REVERT: D 300 MET cc_start: 0.7244 (pmm) cc_final: 0.7021 (pmm) REVERT: D 412 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7554 (ttmm) REVERT: D 420 ILE cc_start: 0.7636 (tp) cc_final: 0.7327 (tp) REVERT: D 421 GLU cc_start: 0.8072 (tp30) cc_final: 0.7839 (tp30) REVERT: E 3 GLN cc_start: 0.8147 (mm110) cc_final: 0.7536 (mm-40) REVERT: E 882 THR cc_start: 0.7734 (t) cc_final: 0.7375 (p) REVERT: F 5 GLN cc_start: 0.7140 (mp10) cc_final: 0.6850 (mp-120) REVERT: F 849 ASP cc_start: 0.7276 (t0) cc_final: 0.7055 (t0) REVERT: F 859 LYS cc_start: 0.7399 (tptp) cc_final: 0.7009 (tptp) REVERT: G 108 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7114 (tm-30) REVERT: G 115 LEU cc_start: 0.7968 (tp) cc_final: 0.7349 (tt) REVERT: G 139 ASN cc_start: 0.6489 (t0) cc_final: 0.6031 (t0) REVERT: G 156 LYS cc_start: 0.8145 (pptt) cc_final: 0.7686 (pptt) REVERT: G 173 HIS cc_start: 0.7934 (m90) cc_final: 0.7338 (m-70) REVERT: H 42 TYR cc_start: 0.6208 (m-80) cc_final: 0.5591 (m-80) REVERT: H 80 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7097 (ptm160) REVERT: H 94 LEU cc_start: 0.8292 (tp) cc_final: 0.7817 (tp) REVERT: H 114 ARG cc_start: 0.7356 (ttt-90) cc_final: 0.6803 (ttp80) REVERT: H 115 LEU cc_start: 0.7885 (tp) cc_final: 0.7647 (tp) REVERT: H 128 ARG cc_start: 0.7274 (ptm160) cc_final: 0.7027 (ptm160) REVERT: I 339 LEU cc_start: 0.8779 (mt) cc_final: 0.8447 (mt) REVERT: I 340 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6828 (mm-30) REVERT: I 341 GLU cc_start: 0.7548 (pt0) cc_final: 0.7152 (pt0) REVERT: I 344 ASP cc_start: 0.7011 (m-30) cc_final: 0.6805 (m-30) REVERT: I 395 MET cc_start: 0.7331 (tmm) cc_final: 0.6924 (tmm) REVERT: I 410 GLU cc_start: 0.8117 (mm-30) cc_final: 0.6971 (mm-30) REVERT: I 412 LYS cc_start: 0.7515 (tptm) cc_final: 0.7089 (tptm) REVERT: I 415 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7363 (tm-30) REVERT: I 419 THR cc_start: 0.7674 (p) cc_final: 0.7433 (p) REVERT: I 421 GLU cc_start: 0.7619 (tp30) cc_final: 0.7389 (tp30) REVERT: I 422 ARG cc_start: 0.7724 (tpt-90) cc_final: 0.6849 (tpp80) REVERT: I 426 GLU cc_start: 0.7009 (mp0) cc_final: 0.5823 (mp0) REVERT: I 435 GLU cc_start: 0.6299 (tp30) cc_final: 0.5922 (tp30) REVERT: I 438 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7325 (mtt90) REVERT: J 378 LEU cc_start: 0.6801 (tt) cc_final: 0.6457 (tp) REVERT: J 388 LEU cc_start: 0.8883 (tt) cc_final: 0.8534 (tt) REVERT: J 389 ARG cc_start: 0.7318 (mtm110) cc_final: 0.7117 (ptp-110) REVERT: J 423 LEU cc_start: 0.7942 (tp) cc_final: 0.7350 (tt) REVERT: J 426 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6660 (mt-10) REVERT: J 431 GLU cc_start: 0.7783 (tp30) cc_final: 0.7445 (tm-30) REVERT: J 435 GLU cc_start: 0.6908 (tp30) cc_final: 0.6314 (tp30) REVERT: J 446 MET cc_start: 0.3702 (tmm) cc_final: 0.3154 (mtt) REVERT: K 5 GLN cc_start: 0.7094 (mp10) cc_final: 0.6838 (mp10) REVERT: K 804 ILE cc_start: 0.7247 (tp) cc_final: 0.6989 (tp) REVERT: K 809 TRP cc_start: 0.7589 (m100) cc_final: 0.6795 (m100) REVERT: K 833 VAL cc_start: 0.8267 (t) cc_final: 0.6884 (t) REVERT: K 837 LYS cc_start: 0.8875 (mttp) cc_final: 0.8588 (mttm) REVERT: K 863 THR cc_start: 0.8535 (t) cc_final: 0.8303 (m) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1603 time to fit residues: 114.6070 Evaluate side-chains 472 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 173 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 174 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN E 805 ASN E 831 ASN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN ** K 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 856 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.153910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.138454 restraints weight = 25898.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.142514 restraints weight = 13475.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.145099 restraints weight = 7785.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.146731 restraints weight = 4887.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.147828 restraints weight = 3314.628| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15139 Z= 0.268 Angle : 0.831 14.041 20371 Z= 0.454 Chirality : 0.047 0.255 2323 Planarity : 0.005 0.073 2759 Dihedral : 4.927 29.438 2184 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.18), residues: 1917 helix: 2.47 (0.12), residues: 1411 sheet: -2.01 (0.41), residues: 140 loop : -1.49 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 41 TYR 0.023 0.003 TYR K 810 PHE 0.014 0.005 PHE A 77 TRP 0.037 0.004 TRP E 809 HIS 0.008 0.002 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00535 (15135) covalent geometry : angle 0.83035 (20363) SS BOND : bond 0.00776 ( 4) SS BOND : angle 2.17657 ( 8) hydrogen bonds : bond 0.05666 ( 1512) hydrogen bonds : angle 4.72003 ( 4500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6726 (m-30) cc_final: 0.6360 (m-30) REVERT: A 151 LEU cc_start: 0.8132 (mt) cc_final: 0.7930 (mt) REVERT: A 152 GLN cc_start: 0.7657 (pp30) cc_final: 0.7425 (pp30) REVERT: A 172 GLU cc_start: 0.6470 (mp0) cc_final: 0.6220 (pm20) REVERT: A 203 ASN cc_start: 0.8034 (m110) cc_final: 0.7548 (m110) REVERT: A 227 LEU cc_start: 0.8450 (mm) cc_final: 0.8243 (mm) REVERT: A 230 LEU cc_start: 0.8302 (mt) cc_final: 0.7917 (mt) REVERT: A 240 GLN cc_start: 0.8120 (tt0) cc_final: 0.7716 (tm-30) REVERT: A 264 ARG cc_start: 0.6878 (mmt180) cc_final: 0.6398 (mmp80) REVERT: B 62 ILE cc_start: 0.6679 (mp) cc_final: 0.6418 (mp) REVERT: B 80 ARG cc_start: 0.5411 (mtm-85) cc_final: 0.3952 (mtm-85) REVERT: B 125 SER cc_start: 0.7591 (t) cc_final: 0.7132 (m) REVERT: B 201 ARG cc_start: 0.7648 (ttt90) cc_final: 0.7341 (ttt90) REVERT: B 226 ASP cc_start: 0.7790 (m-30) cc_final: 0.7261 (m-30) REVERT: B 258 HIS cc_start: 0.5441 (m-70) cc_final: 0.4847 (m-70) REVERT: B 266 ILE cc_start: 0.6398 (tt) cc_final: 0.6124 (tp) REVERT: C 245 ARG cc_start: 0.7521 (ptt180) cc_final: 0.7229 (ptt180) REVERT: C 276 ASN cc_start: 0.7527 (m-40) cc_final: 0.7109 (m-40) REVERT: C 277 ARG cc_start: 0.8170 (tpm170) cc_final: 0.7666 (tpp80) REVERT: C 280 ILE cc_start: 0.7272 (mm) cc_final: 0.6970 (mm) REVERT: C 297 LEU cc_start: 0.8694 (tp) cc_final: 0.8152 (tp) REVERT: C 318 VAL cc_start: 0.7280 (t) cc_final: 0.7047 (t) REVERT: C 393 ASP cc_start: 0.6996 (m-30) cc_final: 0.6709 (m-30) REVERT: C 396 GLN cc_start: 0.6485 (tm-30) cc_final: 0.5363 (tm-30) REVERT: C 400 ASP cc_start: 0.5183 (m-30) cc_final: 0.4456 (m-30) REVERT: C 438 ARG cc_start: 0.6442 (ttm170) cc_final: 0.6233 (ttp-170) REVERT: D 219 ARG cc_start: 0.5868 (mmt-90) cc_final: 0.5510 (mmt180) REVERT: D 265 THR cc_start: 0.8448 (t) cc_final: 0.8133 (p) REVERT: D 272 GLN cc_start: 0.8120 (tt0) cc_final: 0.7346 (mt0) REVERT: D 276 ASN cc_start: 0.7841 (m-40) cc_final: 0.7408 (m-40) REVERT: D 285 THR cc_start: 0.8463 (p) cc_final: 0.8254 (p) REVERT: D 286 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7442 (mtm180) REVERT: D 298 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6561 (mm-30) REVERT: D 299 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 421 GLU cc_start: 0.7958 (tp30) cc_final: 0.7721 (tp30) REVERT: D 429 LEU cc_start: 0.8357 (tt) cc_final: 0.7931 (tp) REVERT: E 3 GLN cc_start: 0.8348 (mm110) cc_final: 0.7720 (mm-40) REVERT: E 808 ARG cc_start: 0.6220 (mtm180) cc_final: 0.5982 (mtm180) REVERT: E 827 TRP cc_start: 0.6776 (p-90) cc_final: 0.6050 (p-90) REVERT: E 831 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6525 (p0) REVERT: E 882 THR cc_start: 0.7704 (t) cc_final: 0.7275 (p) REVERT: F 1 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5355 (tm-30) REVERT: F 859 LYS cc_start: 0.7503 (tptp) cc_final: 0.7235 (tptp) REVERT: F 873 ARG cc_start: 0.7383 (mpt-90) cc_final: 0.6983 (mpt-90) REVERT: F 877 TYR cc_start: 0.6558 (m-10) cc_final: 0.6259 (m-80) REVERT: G 115 LEU cc_start: 0.8005 (tp) cc_final: 0.7471 (tt) REVERT: G 129 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7627 (ttp80) REVERT: G 156 LYS cc_start: 0.8444 (pptt) cc_final: 0.7999 (pptt) REVERT: G 173 HIS cc_start: 0.7835 (m90) cc_final: 0.7445 (m90) REVERT: H 43 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7556 (mm-30) REVERT: H 77 PHE cc_start: 0.5983 (m-10) cc_final: 0.5720 (m-10) REVERT: H 80 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7296 (ptm160) REVERT: H 94 LEU cc_start: 0.8288 (tp) cc_final: 0.6936 (tp) REVERT: H 114 ARG cc_start: 0.7481 (ttt-90) cc_final: 0.6975 (ttp80) REVERT: H 115 LEU cc_start: 0.7971 (tp) cc_final: 0.6775 (tp) REVERT: H 133 ASP cc_start: 0.7913 (m-30) cc_final: 0.7646 (m-30) REVERT: H 176 GLN cc_start: 0.6423 (mp10) cc_final: 0.6203 (mp10) REVERT: I 336 ILE cc_start: 0.8064 (mt) cc_final: 0.7564 (mt) REVERT: I 337 ARG cc_start: 0.7926 (ppt170) cc_final: 0.7724 (ppt170) REVERT: I 340 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6897 (mm-30) REVERT: I 341 GLU cc_start: 0.7587 (pt0) cc_final: 0.7145 (pt0) REVERT: I 395 MET cc_start: 0.7356 (tmm) cc_final: 0.6875 (tmm) REVERT: I 412 LYS cc_start: 0.7540 (tptm) cc_final: 0.7299 (tptm) REVERT: I 415 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7430 (tm-30) REVERT: I 419 THR cc_start: 0.7687 (p) cc_final: 0.7450 (p) REVERT: I 422 ARG cc_start: 0.7617 (tpt-90) cc_final: 0.6622 (tpp80) REVERT: I 426 GLU cc_start: 0.7153 (mp0) cc_final: 0.5894 (mp0) REVERT: I 435 GLU cc_start: 0.6133 (tp30) cc_final: 0.5710 (tp30) REVERT: I 438 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7589 (mtt90) REVERT: J 374 GLN cc_start: 0.7044 (tt0) cc_final: 0.6763 (tt0) REVERT: J 378 LEU cc_start: 0.6930 (tt) cc_final: 0.6524 (tp) REVERT: J 388 LEU cc_start: 0.8932 (tt) cc_final: 0.8516 (tp) REVERT: J 405 ASP cc_start: 0.7175 (m-30) cc_final: 0.6830 (m-30) REVERT: J 409 HIS cc_start: 0.6932 (m-70) cc_final: 0.6446 (m-70) REVERT: J 416 LEU cc_start: 0.8041 (mt) cc_final: 0.7718 (mm) REVERT: J 423 LEU cc_start: 0.8089 (tp) cc_final: 0.7682 (tt) REVERT: J 426 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6730 (mt-10) REVERT: J 431 GLU cc_start: 0.7824 (tp30) cc_final: 0.7183 (tm-30) REVERT: J 435 GLU cc_start: 0.6946 (tp30) cc_final: 0.6326 (tp30) REVERT: J 446 MET cc_start: 0.3731 (tmm) cc_final: 0.3286 (mtt) REVERT: K 805 ASN cc_start: 0.7672 (m-40) cc_final: 0.7322 (t0) REVERT: K 809 TRP cc_start: 0.7845 (m100) cc_final: 0.6864 (m100) REVERT: K 833 VAL cc_start: 0.8356 (t) cc_final: 0.6761 (t) REVERT: K 859 LYS cc_start: 0.8199 (pptt) cc_final: 0.7934 (tmmt) REVERT: K 863 THR cc_start: 0.8646 (t) cc_final: 0.8340 (m) outliers start: 1 outliers final: 0 residues processed: 517 average time/residue: 0.1692 time to fit residues: 116.9488 Evaluate side-chains 471 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 101 optimal weight: 0.0980 chunk 141 optimal weight: 0.2980 chunk 165 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 108 optimal weight: 0.1980 chunk 175 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 HIS J 409 HIS ** K 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.162509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146825 restraints weight = 26051.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.151271 restraints weight = 12712.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.154015 restraints weight = 6912.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.155770 restraints weight = 4093.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.156889 restraints weight = 2628.743| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15139 Z= 0.183 Angle : 0.764 12.069 20371 Z= 0.411 Chirality : 0.045 0.449 2323 Planarity : 0.005 0.056 2759 Dihedral : 4.766 29.666 2184 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.55 (0.18), residues: 1917 helix: 2.79 (0.12), residues: 1418 sheet: -1.92 (0.42), residues: 141 loop : -1.47 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 165 TYR 0.024 0.002 TYR H 42 PHE 0.038 0.004 PHE A 77 TRP 0.027 0.002 TRP E 827 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00373 (15135) covalent geometry : angle 0.76313 (20363) SS BOND : bond 0.00428 ( 4) SS BOND : angle 1.87967 ( 8) hydrogen bonds : bond 0.05384 ( 1512) hydrogen bonds : angle 4.38439 ( 4500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6490 (m-30) cc_final: 0.6023 (m-30) REVERT: A 151 LEU cc_start: 0.8174 (mt) cc_final: 0.7948 (mt) REVERT: A 163 SER cc_start: 0.7710 (t) cc_final: 0.7233 (m) REVERT: A 203 ASN cc_start: 0.8014 (m110) cc_final: 0.7550 (m110) REVERT: A 233 ILE cc_start: 0.7885 (tp) cc_final: 0.7650 (tp) REVERT: A 240 GLN cc_start: 0.7958 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 80 ARG cc_start: 0.5033 (mtm-85) cc_final: 0.4001 (mtm-85) REVERT: B 125 SER cc_start: 0.7628 (t) cc_final: 0.7164 (m) REVERT: B 201 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7449 (ttt90) REVERT: B 209 LEU cc_start: 0.7941 (mm) cc_final: 0.7727 (mp) REVERT: B 226 ASP cc_start: 0.7834 (m-30) cc_final: 0.7283 (m-30) REVERT: B 258 HIS cc_start: 0.5295 (m-70) cc_final: 0.4749 (m-70) REVERT: B 266 ILE cc_start: 0.6757 (tt) cc_final: 0.6468 (tp) REVERT: C 234 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7663 (mm-30) REVERT: C 245 ARG cc_start: 0.7549 (ptt180) cc_final: 0.7209 (ptt180) REVERT: C 258 HIS cc_start: 0.6970 (t-90) cc_final: 0.6718 (t-90) REVERT: C 266 ILE cc_start: 0.8261 (tp) cc_final: 0.8041 (tp) REVERT: C 272 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7408 (mm-40) REVERT: C 276 ASN cc_start: 0.7480 (m-40) cc_final: 0.7159 (m-40) REVERT: C 277 ARG cc_start: 0.8349 (tpm170) cc_final: 0.7912 (tpp80) REVERT: C 280 ILE cc_start: 0.7378 (mm) cc_final: 0.7136 (mm) REVERT: C 286 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7925 (mtm110) REVERT: C 329 LEU cc_start: 0.6181 (tp) cc_final: 0.5819 (tt) REVERT: C 393 ASP cc_start: 0.6959 (m-30) cc_final: 0.6696 (m-30) REVERT: C 396 GLN cc_start: 0.6237 (tm-30) cc_final: 0.5165 (tm-30) REVERT: C 400 ASP cc_start: 0.5452 (m-30) cc_final: 0.4618 (m-30) REVERT: C 404 ARG cc_start: 0.8399 (ptt90) cc_final: 0.7957 (ptp90) REVERT: C 410 GLU cc_start: 0.7772 (tp30) cc_final: 0.7227 (tp30) REVERT: C 438 ARG cc_start: 0.6590 (ttm170) cc_final: 0.6109 (mtp85) REVERT: D 265 THR cc_start: 0.8440 (t) cc_final: 0.8116 (p) REVERT: D 266 ILE cc_start: 0.8122 (mm) cc_final: 0.7823 (pt) REVERT: D 272 GLN cc_start: 0.8313 (tt0) cc_final: 0.7675 (tt0) REVERT: D 276 ASN cc_start: 0.7876 (m-40) cc_final: 0.7221 (m-40) REVERT: D 299 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7374 (mm-30) REVERT: D 384 ARG cc_start: 0.7530 (ptm-80) cc_final: 0.7313 (ptm-80) REVERT: D 420 ILE cc_start: 0.7596 (tp) cc_final: 0.7183 (tp) REVERT: D 421 GLU cc_start: 0.8011 (tp30) cc_final: 0.7708 (tp30) REVERT: D 429 LEU cc_start: 0.8372 (tt) cc_final: 0.7971 (tp) REVERT: E 3 GLN cc_start: 0.8151 (mm110) cc_final: 0.7509 (mm-40) REVERT: E 844 ARG cc_start: 0.7377 (ttp80) cc_final: 0.6786 (ttp-170) REVERT: E 877 TYR cc_start: 0.6880 (m-80) cc_final: 0.6357 (m-80) REVERT: F 1 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5527 (tm-30) REVERT: F 800 SER cc_start: 0.8677 (m) cc_final: 0.8235 (m) REVERT: F 849 ASP cc_start: 0.7368 (t0) cc_final: 0.7143 (t0) REVERT: F 859 LYS cc_start: 0.7539 (tptp) cc_final: 0.7229 (tptp) REVERT: F 873 ARG cc_start: 0.7403 (mpt-90) cc_final: 0.6912 (mpt-90) REVERT: G 139 ASN cc_start: 0.6444 (t0) cc_final: 0.5998 (t0) REVERT: G 156 LYS cc_start: 0.8293 (pptt) cc_final: 0.7854 (pptt) REVERT: G 157 VAL cc_start: 0.8340 (t) cc_final: 0.7874 (t) REVERT: G 173 HIS cc_start: 0.8026 (m90) cc_final: 0.7629 (m90) REVERT: H 43 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7649 (mm-30) REVERT: H 80 ARG cc_start: 0.7600 (ptm160) cc_final: 0.7284 (ptm160) REVERT: H 133 ASP cc_start: 0.8068 (m-30) cc_final: 0.7848 (m-30) REVERT: I 340 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6908 (mm-30) REVERT: I 341 GLU cc_start: 0.7503 (pt0) cc_final: 0.7057 (pt0) REVERT: I 409 HIS cc_start: 0.7183 (t70) cc_final: 0.6629 (t-90) REVERT: I 410 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7125 (mm-30) REVERT: I 412 LYS cc_start: 0.7502 (tptm) cc_final: 0.7118 (tptm) REVERT: I 415 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7438 (tm-30) REVERT: I 421 GLU cc_start: 0.7611 (tp30) cc_final: 0.7336 (tp30) REVERT: I 422 ARG cc_start: 0.7624 (tpt-90) cc_final: 0.6730 (tpp80) REVERT: I 426 GLU cc_start: 0.7037 (mp0) cc_final: 0.5679 (mp0) REVERT: I 435 GLU cc_start: 0.5880 (tp30) cc_final: 0.5610 (tp30) REVERT: J 374 GLN cc_start: 0.6981 (tt0) cc_final: 0.6733 (tt0) REVERT: J 378 LEU cc_start: 0.6842 (tt) cc_final: 0.6481 (tp) REVERT: J 388 LEU cc_start: 0.8901 (tt) cc_final: 0.8571 (tt) REVERT: J 423 LEU cc_start: 0.7958 (tp) cc_final: 0.7367 (tt) REVERT: J 426 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6634 (mt-10) REVERT: J 431 GLU cc_start: 0.7879 (tp30) cc_final: 0.7495 (tm-30) REVERT: J 435 GLU cc_start: 0.7057 (tp30) cc_final: 0.6412 (tp30) REVERT: J 446 MET cc_start: 0.3552 (tmm) cc_final: 0.3025 (mtt) REVERT: K 833 VAL cc_start: 0.8239 (t) cc_final: 0.6868 (t) REVERT: K 855 MET cc_start: 0.6191 (mpp) cc_final: 0.5930 (mpp) REVERT: L 807 MET cc_start: 0.7897 (pmm) cc_final: 0.7679 (pmm) REVERT: L 824 VAL cc_start: 0.8277 (m) cc_final: 0.7853 (m) REVERT: L 839 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8231 (mtp85) REVERT: L 844 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7088 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1646 time to fit residues: 115.5547 Evaluate side-chains 481 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 147 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 179 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 145 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 249 GLN E 805 ASN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 409 HIS ** K 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.157246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.141716 restraints weight = 25806.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.145907 restraints weight = 12966.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.148518 restraints weight = 7239.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.150148 restraints weight = 4420.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.151230 restraints weight = 2939.973| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15139 Z= 0.178 Angle : 0.770 11.584 20371 Z= 0.413 Chirality : 0.044 0.419 2323 Planarity : 0.005 0.049 2759 Dihedral : 4.685 29.756 2184 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.65 (0.19), residues: 1917 helix: 2.87 (0.12), residues: 1416 sheet: -1.80 (0.40), residues: 163 loop : -1.41 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 232 TYR 0.035 0.002 TYR H 42 PHE 0.036 0.005 PHE A 77 TRP 0.020 0.002 TRP E 827 HIS 0.009 0.001 HIS J 409 Details of bonding type rmsd covalent geometry : bond 0.00361 (15135) covalent geometry : angle 0.76917 (20363) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.76036 ( 8) hydrogen bonds : bond 0.05335 ( 1512) hydrogen bonds : angle 4.33250 ( 4500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6567 (m-30) cc_final: 0.6323 (m-30) REVERT: A 151 LEU cc_start: 0.8154 (mt) cc_final: 0.7927 (mt) REVERT: A 163 SER cc_start: 0.7781 (t) cc_final: 0.7347 (m) REVERT: A 203 ASN cc_start: 0.8019 (m110) cc_final: 0.7548 (m110) REVERT: A 227 LEU cc_start: 0.8473 (mm) cc_final: 0.8267 (mm) REVERT: A 230 LEU cc_start: 0.8307 (mt) cc_final: 0.7950 (mt) REVERT: A 236 ASP cc_start: 0.7747 (t0) cc_final: 0.7521 (t70) REVERT: B 62 ILE cc_start: 0.6648 (mp) cc_final: 0.6429 (mp) REVERT: B 80 ARG cc_start: 0.4987 (mtm-85) cc_final: 0.3895 (mtm-85) REVERT: B 107 GLU cc_start: 0.7077 (tt0) cc_final: 0.6748 (tt0) REVERT: B 226 ASP cc_start: 0.7814 (m-30) cc_final: 0.7268 (m-30) REVERT: B 247 ARG cc_start: 0.8236 (mmp80) cc_final: 0.7946 (mmm160) REVERT: B 258 HIS cc_start: 0.5162 (m-70) cc_final: 0.4676 (m-70) REVERT: B 266 ILE cc_start: 0.6826 (tt) cc_final: 0.6539 (tp) REVERT: C 234 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7598 (mm-30) REVERT: C 245 ARG cc_start: 0.7554 (ptt180) cc_final: 0.7210 (ptt180) REVERT: C 258 HIS cc_start: 0.6899 (t-90) cc_final: 0.6667 (t-90) REVERT: C 266 ILE cc_start: 0.8258 (tp) cc_final: 0.7983 (tp) REVERT: C 272 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7446 (mm-40) REVERT: C 276 ASN cc_start: 0.7503 (m-40) cc_final: 0.7227 (m-40) REVERT: C 277 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7610 (tpm170) REVERT: C 286 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7622 (ptt90) REVERT: C 393 ASP cc_start: 0.6836 (m-30) cc_final: 0.6595 (m-30) REVERT: C 396 GLN cc_start: 0.6303 (tm-30) cc_final: 0.5376 (tm-30) REVERT: C 400 ASP cc_start: 0.5349 (m-30) cc_final: 0.4730 (m-30) REVERT: C 404 ARG cc_start: 0.8374 (ptt90) cc_final: 0.7935 (ptp90) REVERT: C 410 GLU cc_start: 0.7736 (tp30) cc_final: 0.7207 (tp30) REVERT: C 438 ARG cc_start: 0.6701 (ttm170) cc_final: 0.6427 (ttm170) REVERT: D 266 ILE cc_start: 0.8133 (mm) cc_final: 0.7900 (pt) REVERT: D 272 GLN cc_start: 0.8274 (tt0) cc_final: 0.7556 (tt0) REVERT: D 276 ASN cc_start: 0.7877 (m-40) cc_final: 0.7244 (m-40) REVERT: D 277 ARG cc_start: 0.7849 (tpt-90) cc_final: 0.7427 (tpt-90) REVERT: D 299 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 303 GLN cc_start: 0.7747 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 384 ARG cc_start: 0.7498 (ptm-80) cc_final: 0.7256 (ptm-80) REVERT: D 421 GLU cc_start: 0.7995 (tp30) cc_final: 0.7602 (tp30) REVERT: D 429 LEU cc_start: 0.8332 (tt) cc_final: 0.7952 (tp) REVERT: D 446 MET cc_start: 0.6873 (mmp) cc_final: 0.6624 (mmp) REVERT: E 801 ILE cc_start: 0.8040 (mm) cc_final: 0.7835 (mm) REVERT: E 844 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7086 (ttp-170) REVERT: E 877 TYR cc_start: 0.6842 (m-80) cc_final: 0.6389 (m-80) REVERT: F 1 GLU cc_start: 0.6278 (tm-30) cc_final: 0.5530 (tm-30) REVERT: F 859 LYS cc_start: 0.7344 (tptp) cc_final: 0.7061 (tptp) REVERT: F 873 ARG cc_start: 0.7385 (mpt-90) cc_final: 0.6932 (mpt-90) REVERT: G 139 ASN cc_start: 0.6470 (t0) cc_final: 0.6224 (t0) REVERT: G 156 LYS cc_start: 0.8293 (pptt) cc_final: 0.7832 (pptt) REVERT: G 174 LEU cc_start: 0.8056 (mt) cc_final: 0.7805 (mm) REVERT: H 42 TYR cc_start: 0.5945 (m-80) cc_final: 0.5734 (m-80) REVERT: H 43 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7581 (mm-30) REVERT: H 80 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7267 (ptm160) REVERT: H 115 LEU cc_start: 0.7858 (tp) cc_final: 0.6681 (tp) REVERT: H 133 ASP cc_start: 0.8030 (m-30) cc_final: 0.7819 (m-30) REVERT: I 336 ILE cc_start: 0.7901 (mt) cc_final: 0.7483 (mt) REVERT: I 340 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6853 (mm-30) REVERT: I 341 GLU cc_start: 0.7474 (pt0) cc_final: 0.7039 (pt0) REVERT: I 410 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7112 (mm-30) REVERT: I 412 LYS cc_start: 0.7482 (tptm) cc_final: 0.7177 (tptm) REVERT: I 415 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7321 (tm-30) REVERT: I 419 THR cc_start: 0.7671 (p) cc_final: 0.7457 (p) REVERT: I 422 ARG cc_start: 0.7555 (tpt-90) cc_final: 0.6762 (tpp80) REVERT: I 426 GLU cc_start: 0.7057 (mp0) cc_final: 0.5780 (mp0) REVERT: I 435 GLU cc_start: 0.6199 (tp30) cc_final: 0.5856 (tp30) REVERT: I 438 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7450 (mtm-85) REVERT: J 378 LEU cc_start: 0.6876 (tt) cc_final: 0.6555 (tp) REVERT: J 388 LEU cc_start: 0.8853 (tt) cc_final: 0.8499 (tt) REVERT: J 423 LEU cc_start: 0.7856 (tp) cc_final: 0.7342 (tt) REVERT: J 426 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6682 (mt-10) REVERT: J 431 GLU cc_start: 0.7831 (tp30) cc_final: 0.7527 (tm-30) REVERT: J 435 GLU cc_start: 0.7022 (tp30) cc_final: 0.6380 (tp30) REVERT: J 446 MET cc_start: 0.3556 (tmm) cc_final: 0.3017 (mtt) REVERT: K 4 LEU cc_start: 0.7703 (mt) cc_final: 0.7223 (mt) REVERT: K 5 GLN cc_start: 0.7328 (mm110) cc_final: 0.6806 (mm110) REVERT: K 809 TRP cc_start: 0.7753 (m100) cc_final: 0.6816 (m100) REVERT: K 833 VAL cc_start: 0.8225 (t) cc_final: 0.6941 (t) REVERT: K 855 MET cc_start: 0.6002 (mpp) cc_final: 0.5777 (mpp) REVERT: K 861 GLU cc_start: 0.7621 (pp20) cc_final: 0.6906 (pp20) REVERT: K 863 THR cc_start: 0.8250 (m) cc_final: 0.8043 (m) REVERT: L 807 MET cc_start: 0.7818 (pmm) cc_final: 0.7608 (pmm) REVERT: L 824 VAL cc_start: 0.8261 (m) cc_final: 0.8042 (m) REVERT: L 839 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8301 (mtp85) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.1598 time to fit residues: 110.0899 Evaluate side-chains 475 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 99 optimal weight: 0.0270 chunk 130 optimal weight: 0.5980 chunk 85 optimal weight: 0.0870 chunk 73 optimal weight: 0.0980 chunk 181 optimal weight: 0.4980 chunk 140 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 253 ASN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN ** K 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.155791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139741 restraints weight = 25975.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.144095 restraints weight = 13033.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.146805 restraints weight = 7317.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.148505 restraints weight = 4483.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.149598 restraints weight = 2979.313| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15139 Z= 0.206 Angle : 0.793 11.672 20371 Z= 0.430 Chirality : 0.045 0.257 2323 Planarity : 0.005 0.053 2759 Dihedral : 4.782 31.346 2184 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.40 (0.18), residues: 1917 helix: 2.67 (0.12), residues: 1414 sheet: -1.80 (0.40), residues: 162 loop : -1.47 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 404 TYR 0.043 0.002 TYR H 42 PHE 0.021 0.004 PHE A 77 TRP 0.037 0.003 TRP L 827 HIS 0.009 0.002 HIS J 409 Details of bonding type rmsd covalent geometry : bond 0.00423 (15135) covalent geometry : angle 0.79265 (20363) SS BOND : bond 0.00524 ( 4) SS BOND : angle 1.81996 ( 8) hydrogen bonds : bond 0.05405 ( 1512) hydrogen bonds : angle 4.46754 ( 4500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6630 (m-30) cc_final: 0.6368 (m-30) REVERT: A 151 LEU cc_start: 0.8141 (mt) cc_final: 0.7926 (mt) REVERT: A 161 ASP cc_start: 0.6439 (t70) cc_final: 0.6144 (t70) REVERT: A 163 SER cc_start: 0.7781 (t) cc_final: 0.7336 (m) REVERT: A 170 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7140 (ttt-90) REVERT: A 203 ASN cc_start: 0.8021 (m110) cc_final: 0.7574 (m110) REVERT: A 230 LEU cc_start: 0.8291 (mt) cc_final: 0.7934 (mt) REVERT: A 236 ASP cc_start: 0.7759 (t0) cc_final: 0.7550 (t70) REVERT: A 240 GLN cc_start: 0.8171 (tt0) cc_final: 0.7823 (tm-30) REVERT: B 80 ARG cc_start: 0.5016 (mtm-85) cc_final: 0.4053 (mtm-85) REVERT: B 110 GLU cc_start: 0.6959 (pp20) cc_final: 0.6721 (pp20) REVERT: B 125 SER cc_start: 0.7731 (t) cc_final: 0.7255 (m) REVERT: B 171 ILE cc_start: 0.7177 (tt) cc_final: 0.6610 (tt) REVERT: B 226 ASP cc_start: 0.7808 (m-30) cc_final: 0.7299 (m-30) REVERT: B 247 ARG cc_start: 0.8197 (mmp80) cc_final: 0.7657 (mmm160) REVERT: B 258 HIS cc_start: 0.5191 (m-70) cc_final: 0.4719 (m-70) REVERT: B 266 ILE cc_start: 0.6775 (tt) cc_final: 0.6474 (tp) REVERT: C 234 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7574 (mm-30) REVERT: C 245 ARG cc_start: 0.7530 (ptt180) cc_final: 0.7213 (ptt180) REVERT: C 258 HIS cc_start: 0.6879 (t-90) cc_final: 0.6666 (t-90) REVERT: C 266 ILE cc_start: 0.8348 (tp) cc_final: 0.6853 (tp) REVERT: C 276 ASN cc_start: 0.7595 (m-40) cc_final: 0.7281 (m-40) REVERT: C 277 ARG cc_start: 0.8293 (tpm170) cc_final: 0.7630 (tpm170) REVERT: C 286 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7815 (mtm110) REVERT: C 321 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7547 (tmm-80) REVERT: C 393 ASP cc_start: 0.6879 (m-30) cc_final: 0.6621 (m-30) REVERT: C 396 GLN cc_start: 0.6208 (tm-30) cc_final: 0.5295 (tm-30) REVERT: C 400 ASP cc_start: 0.5273 (m-30) cc_final: 0.4861 (m-30) REVERT: C 438 ARG cc_start: 0.6806 (ttm170) cc_final: 0.6250 (mtp180) REVERT: D 247 ARG cc_start: 0.7549 (mmp-170) cc_final: 0.7087 (mmm160) REVERT: D 265 THR cc_start: 0.8435 (t) cc_final: 0.8163 (p) REVERT: D 266 ILE cc_start: 0.8160 (mm) cc_final: 0.7873 (pt) REVERT: D 272 GLN cc_start: 0.8271 (tt0) cc_final: 0.7554 (tt0) REVERT: D 276 ASN cc_start: 0.7861 (m-40) cc_final: 0.7439 (m-40) REVERT: D 286 ARG cc_start: 0.7340 (mmp80) cc_final: 0.7086 (mmp80) REVERT: D 299 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7258 (mm-30) REVERT: D 303 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7361 (tm-30) REVERT: D 318 VAL cc_start: 0.7663 (t) cc_final: 0.7424 (m) REVERT: D 384 ARG cc_start: 0.7510 (ptm-80) cc_final: 0.7262 (ptm-80) REVERT: D 420 ILE cc_start: 0.7760 (tp) cc_final: 0.7325 (tp) REVERT: D 421 GLU cc_start: 0.7925 (tp30) cc_final: 0.7680 (tp30) REVERT: D 429 LEU cc_start: 0.8354 (tt) cc_final: 0.7952 (tp) REVERT: D 446 MET cc_start: 0.6513 (mmp) cc_final: 0.6149 (mmp) REVERT: E 801 ILE cc_start: 0.8044 (mm) cc_final: 0.7826 (mm) REVERT: E 802 ASP cc_start: 0.7151 (t0) cc_final: 0.6867 (t0) REVERT: E 882 THR cc_start: 0.7831 (t) cc_final: 0.7248 (p) REVERT: F 1 GLU cc_start: 0.6370 (tm-30) cc_final: 0.5592 (tm-30) REVERT: F 859 LYS cc_start: 0.7350 (tptp) cc_final: 0.7083 (tptp) REVERT: F 873 ARG cc_start: 0.7400 (mpt-90) cc_final: 0.6944 (mpt-90) REVERT: G 133 ASP cc_start: 0.7348 (t70) cc_final: 0.6970 (t0) REVERT: G 139 ASN cc_start: 0.6570 (t0) cc_final: 0.6280 (t0) REVERT: G 156 LYS cc_start: 0.8335 (pptt) cc_final: 0.7912 (pptt) REVERT: G 157 VAL cc_start: 0.8367 (t) cc_final: 0.7867 (t) REVERT: G 173 HIS cc_start: 0.8113 (m90) cc_final: 0.7675 (m90) REVERT: G 174 LEU cc_start: 0.8050 (mt) cc_final: 0.7792 (mm) REVERT: H 42 TYR cc_start: 0.6327 (m-80) cc_final: 0.5716 (m-10) REVERT: H 43 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7627 (mm-30) REVERT: H 80 ARG cc_start: 0.7551 (ptm160) cc_final: 0.7233 (ptm160) REVERT: H 115 LEU cc_start: 0.7741 (tp) cc_final: 0.6750 (tp) REVERT: H 133 ASP cc_start: 0.8033 (m-30) cc_final: 0.7745 (m-30) REVERT: I 339 LEU cc_start: 0.8754 (mt) cc_final: 0.8511 (mp) REVERT: I 340 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6865 (mm-30) REVERT: I 341 GLU cc_start: 0.7609 (pt0) cc_final: 0.7147 (pt0) REVERT: I 410 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7125 (mm-30) REVERT: I 412 LYS cc_start: 0.7487 (tptm) cc_final: 0.7153 (tptm) REVERT: I 415 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7313 (tm-30) REVERT: I 419 THR cc_start: 0.7762 (p) cc_final: 0.7540 (p) REVERT: I 422 ARG cc_start: 0.7551 (tpt-90) cc_final: 0.6710 (tpp80) REVERT: I 426 GLU cc_start: 0.7152 (mp0) cc_final: 0.5772 (mp0) REVERT: I 435 GLU cc_start: 0.6262 (tp30) cc_final: 0.5631 (tp30) REVERT: J 374 GLN cc_start: 0.6998 (tt0) cc_final: 0.6778 (tt0) REVERT: J 378 LEU cc_start: 0.6914 (tt) cc_final: 0.6566 (tp) REVERT: J 388 LEU cc_start: 0.8850 (tt) cc_final: 0.8490 (tt) REVERT: J 423 LEU cc_start: 0.7905 (tp) cc_final: 0.7408 (tt) REVERT: J 426 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6668 (mt-10) REVERT: J 431 GLU cc_start: 0.7857 (tp30) cc_final: 0.7430 (tm-30) REVERT: J 435 GLU cc_start: 0.6961 (tp30) cc_final: 0.6375 (tp30) REVERT: J 446 MET cc_start: 0.3635 (tmm) cc_final: 0.3088 (mtt) REVERT: K 790 SER cc_start: 0.6490 (p) cc_final: 0.6241 (p) REVERT: K 804 ILE cc_start: 0.8094 (mp) cc_final: 0.7860 (mp) REVERT: K 833 VAL cc_start: 0.8218 (t) cc_final: 0.6910 (t) REVERT: K 855 MET cc_start: 0.5884 (mpp) cc_final: 0.5626 (mpp) REVERT: K 863 THR cc_start: 0.8367 (m) cc_final: 0.8111 (m) REVERT: K 885 THR cc_start: 0.4139 (m) cc_final: 0.3870 (m) REVERT: L 807 MET cc_start: 0.7804 (pmm) cc_final: 0.7547 (pmm) REVERT: L 839 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7699 (mtp85) REVERT: L 844 ARG cc_start: 0.7354 (ttp-110) cc_final: 0.7142 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.1656 time to fit residues: 112.6099 Evaluate side-chains 477 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 0.4980 chunk 6 optimal weight: 0.0970 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 0.0870 chunk 177 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS E 805 ASN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.156236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.139487 restraints weight = 25898.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.143944 restraints weight = 13330.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.146754 restraints weight = 7618.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.148541 restraints weight = 4745.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.149709 restraints weight = 3201.980| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15139 Z= 0.244 Angle : 0.843 12.694 20371 Z= 0.458 Chirality : 0.047 0.354 2323 Planarity : 0.006 0.137 2759 Dihedral : 4.934 31.642 2184 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.13 (0.18), residues: 1917 helix: 2.42 (0.12), residues: 1412 sheet: -1.80 (0.41), residues: 161 loop : -1.34 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 41 TYR 0.034 0.002 TYR H 42 PHE 0.044 0.005 PHE A 77 TRP 0.038 0.004 TRP L 827 HIS 0.010 0.002 HIS J 409 Details of bonding type rmsd covalent geometry : bond 0.00497 (15135) covalent geometry : angle 0.84241 (20363) SS BOND : bond 0.00583 ( 4) SS BOND : angle 2.12067 ( 8) hydrogen bonds : bond 0.05572 ( 1512) hydrogen bonds : angle 4.64441 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.17 seconds wall clock time: 61 minutes 1.62 seconds (3661.62 seconds total)