Starting phenix.real_space_refine on Wed Mar 4 11:30:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oks_20103/03_2026/6oks_20103.map" } resolution = 4.2 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= 0.001 sd= 0.005 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 56 5.16 5 C 8428 2.51 5 N 2184 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13244 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 946 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 1.41, per 1000 atoms: 0.11 Number of scatterers: 13244 At special positions: 0 Unit cell: (126.15, 121.8, 89.9, 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 56 16.00 O 2576 8.00 N 2184 7.00 C 8428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.00 Conformation dependent library (CDL) restraints added in 733.4 milliseconds 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 28 sheets defined 5.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.539A pdb=" N MET A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'E' and resid 759 through 764 Processing helix chain 'F' and resid 759 through 764 Processing helix chain 'G' and resid 759 through 764 Processing helix chain 'H' and resid 759 through 764 Processing helix chain 'I' and resid 759 through 764 Processing helix chain 'J' and resid 759 through 764 Processing helix chain 'K' and resid 759 through 764 Processing helix chain 'L' and resid 759 through 764 Processing helix chain 'M' and resid 759 through 764 Processing helix chain 'N' and resid 759 through 764 Processing sheet with id=AA1, first strand: chain 'A' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY A 785 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN A 773 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE A 783 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP A 817 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA A 808 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 819 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 806 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU A 858 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY B 785 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN B 773 " --> pdb=" O ILE B 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE B 783 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP B 817 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA B 808 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 819 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 806 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 858 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY C 785 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN C 773 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE C 783 " --> pdb=" O ASN C 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP C 817 " --> pdb=" O ALA C 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA C 808 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY C 819 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 806 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU C 858 " --> pdb=" O GLU C 869 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY D 785 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 773 " --> pdb=" O ILE D 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 783 " --> pdb=" O ASN D 773 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP D 817 " --> pdb=" O ALA D 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA D 808 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY D 819 " --> pdb=" O VAL D 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 806 " --> pdb=" O GLY D 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 858 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY E 785 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN E 773 " --> pdb=" O ILE E 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 783 " --> pdb=" O ASN E 773 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP E 817 " --> pdb=" O ALA E 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA E 808 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY E 819 " --> pdb=" O VAL E 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL E 806 " --> pdb=" O GLY E 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU E 858 " --> pdb=" O GLU E 869 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY F 785 " --> pdb=" O ASP F 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN F 773 " --> pdb=" O ILE F 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE F 783 " --> pdb=" O ASN F 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP F 817 " --> pdb=" O ALA F 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA F 808 " --> pdb=" O ASP F 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY F 819 " --> pdb=" O VAL F 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 806 " --> pdb=" O GLY F 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU F 858 " --> pdb=" O GLU F 869 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY G 785 " --> pdb=" O ASP G 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN G 773 " --> pdb=" O ILE G 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE G 783 " --> pdb=" O ASN G 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP G 817 " --> pdb=" O ALA G 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA G 808 " --> pdb=" O ASP G 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY G 819 " --> pdb=" O VAL G 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL G 806 " --> pdb=" O GLY G 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU G 858 " --> pdb=" O GLU G 869 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY H 785 " --> pdb=" O ASP H 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN H 773 " --> pdb=" O ILE H 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE H 783 " --> pdb=" O ASN H 773 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP H 817 " --> pdb=" O ALA H 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA H 808 " --> pdb=" O ASP H 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY H 819 " --> pdb=" O VAL H 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 806 " --> pdb=" O GLY H 819 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU H 858 " --> pdb=" O GLU H 869 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY I 785 " --> pdb=" O ASP I 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN I 773 " --> pdb=" O ILE I 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE I 783 " --> pdb=" O ASN I 773 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP I 817 " --> pdb=" O ALA I 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA I 808 " --> pdb=" O ASP I 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY I 819 " --> pdb=" O VAL I 806 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 806 " --> pdb=" O GLY I 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU I 858 " --> pdb=" O GLU I 869 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY J 785 " --> pdb=" O ASP J 771 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN J 773 " --> pdb=" O ILE J 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE J 783 " --> pdb=" O ASN J 773 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP J 817 " --> pdb=" O ALA J 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA J 808 " --> pdb=" O ASP J 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY J 819 " --> pdb=" O VAL J 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL J 806 " --> pdb=" O GLY J 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU J 858 " --> pdb=" O GLU J 869 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY K 785 " --> pdb=" O ASP K 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN K 773 " --> pdb=" O ILE K 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE K 783 " --> pdb=" O ASN K 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP K 817 " --> pdb=" O ALA K 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA K 808 " --> pdb=" O ASP K 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY K 819 " --> pdb=" O VAL K 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL K 806 " --> pdb=" O GLY K 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU K 858 " --> pdb=" O GLU K 869 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY L 785 " --> pdb=" O ASP L 771 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN L 773 " --> pdb=" O ILE L 783 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE L 783 " --> pdb=" O ASN L 773 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP L 817 " --> pdb=" O ALA L 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA L 808 " --> pdb=" O ASP L 817 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY L 819 " --> pdb=" O VAL L 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL L 806 " --> pdb=" O GLY L 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU L 858 " --> pdb=" O GLU L 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 768 through 774 removed outlier: 3.652A pdb=" N GLY M 785 " --> pdb=" O ASP M 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN M 773 " --> pdb=" O ILE M 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE M 783 " --> pdb=" O ASN M 773 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 815 through 822 removed outlier: 6.521A pdb=" N ASP M 817 " --> pdb=" O ALA M 808 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA M 808 " --> pdb=" O ASP M 817 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY M 819 " --> pdb=" O VAL M 806 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL M 806 " --> pdb=" O GLY M 819 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU M 858 " --> pdb=" O GLU M 869 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 768 through 774 removed outlier: 3.653A pdb=" N GLY N 785 " --> pdb=" O ASP N 771 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN N 773 " --> pdb=" O ILE N 783 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE N 783 " --> pdb=" O ASN N 773 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 815 through 822 removed outlier: 6.522A pdb=" N ASP N 817 " --> pdb=" O ALA N 808 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA N 808 " --> pdb=" O ASP N 817 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY N 819 " --> pdb=" O VAL N 806 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL N 806 " --> pdb=" O GLY N 819 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU N 858 " --> pdb=" O GLU N 869 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4256 1.34 - 1.46: 2884 1.46 - 1.57: 6272 1.57 - 1.69: 14 1.69 - 1.81: 112 Bond restraints: 13538 Sorted by residual: bond pdb=" C ARG N 805 " pdb=" N VAL N 806 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.56e-02 4.11e+03 4.50e+00 bond pdb=" C ARG K 805 " pdb=" N VAL K 806 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.56e-02 4.11e+03 4.47e+00 bond pdb=" C ARG L 805 " pdb=" N VAL L 806 " ideal model delta sigma weight residual 1.330 1.298 0.033 1.56e-02 4.11e+03 4.42e+00 bond pdb=" C ARG G 805 " pdb=" N VAL G 806 " ideal model delta sigma weight residual 1.330 1.298 0.033 1.56e-02 4.11e+03 4.36e+00 bond pdb=" C ARG H 805 " pdb=" N VAL H 806 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.56e-02 4.11e+03 4.33e+00 ... (remaining 13533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17071 2.04 - 4.07: 967 4.07 - 6.11: 204 6.11 - 8.14: 14 8.14 - 10.18: 42 Bond angle restraints: 18298 Sorted by residual: angle pdb=" CB GLU L 824 " pdb=" CG GLU L 824 " pdb=" CD GLU L 824 " ideal model delta sigma weight residual 112.60 121.58 -8.98 1.70e+00 3.46e-01 2.79e+01 angle pdb=" CB GLU C 824 " pdb=" CG GLU C 824 " pdb=" CD GLU C 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU A 824 " pdb=" CG GLU A 824 " pdb=" CD GLU A 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU N 824 " pdb=" CG GLU N 824 " pdb=" CD GLU N 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 angle pdb=" CB GLU I 824 " pdb=" CG GLU I 824 " pdb=" CD GLU I 824 " ideal model delta sigma weight residual 112.60 121.56 -8.96 1.70e+00 3.46e-01 2.78e+01 ... (remaining 18293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 6664 13.87 - 27.75: 915 27.75 - 41.62: 317 41.62 - 55.49: 196 55.49 - 69.36: 56 Dihedral angle restraints: 8148 sinusoidal: 3374 harmonic: 4774 Sorted by residual: dihedral pdb=" CA TYR K 861 " pdb=" C TYR K 861 " pdb=" N ALA K 862 " pdb=" CA ALA K 862 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASP F 758 " pdb=" C ASP F 758 " pdb=" N GLN F 759 " pdb=" CA GLN F 759 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TYR D 861 " pdb=" C TYR D 861 " pdb=" N ALA D 862 " pdb=" CA ALA D 862 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 8145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1061 0.036 - 0.072: 526 0.072 - 0.108: 192 0.108 - 0.144: 125 0.144 - 0.180: 14 Chirality restraints: 1918 Sorted by residual: chirality pdb=" CB ILE D 801 " pdb=" CA ILE D 801 " pdb=" CG1 ILE D 801 " pdb=" CG2 ILE D 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CB ILE E 801 " pdb=" CA ILE E 801 " pdb=" CG1 ILE E 801 " pdb=" CG2 ILE E 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CB ILE H 801 " pdb=" CA ILE H 801 " pdb=" CG1 ILE H 801 " pdb=" CG2 ILE H 801 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1915 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 864 " -0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO E 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 865 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 864 " -0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO M 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO M 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 865 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 864 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO F 865 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 865 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 865 " -0.045 5.00e-02 4.00e+02 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4200 2.82 - 3.34: 10897 3.34 - 3.86: 21318 3.86 - 4.38: 22480 4.38 - 4.90: 38628 Nonbonded interactions: 97523 Sorted by model distance: nonbonded pdb=" NE2 HIS M 765 " pdb=" OE2 GLU M 869 " model vdw 2.299 3.120 nonbonded pdb=" NE2 HIS G 765 " pdb=" OE2 GLU G 869 " model vdw 2.299 3.120 nonbonded pdb=" NE2 HIS A 765 " pdb=" OE2 GLU A 869 " model vdw 2.299 3.120 nonbonded pdb=" NE2 HIS K 765 " pdb=" OE2 GLU K 869 " model vdw 2.299 3.120 nonbonded pdb=" NE2 HIS B 765 " pdb=" OE2 GLU B 869 " model vdw 2.299 3.120 ... (remaining 97518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.008 0.055 13538 Z= 0.382 Angle : 1.152 10.178 18298 Z= 0.655 Chirality : 0.053 0.180 1918 Planarity : 0.009 0.079 2394 Dihedral : 17.363 69.364 5124 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 9.80 % Allowed : 6.86 % Favored : 83.33 % 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: -5.50 (0.15), residues: 1582 helix: -4.78 (0.17), residues: 182 sheet: -2.21 (0.36), residues: 168 loop : -4.08 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 868 TYR 0.018 0.002 TYR I 855 PHE 0.015 0.002 PHE M 774 HIS 0.008 0.005 HIS H 765 Details of bonding type rmsd covalent geometry : bond 0.00793 (13538) covalent geometry : angle 1.15180 (18298) hydrogen bonds : bond 0.19580 ( 280) hydrogen bonds : angle 11.88876 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 534 time to evaluate : 0.503 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: A 759 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 762 MET cc_start: 0.6611 (mtt) cc_final: 0.6092 (mtt) REVERT: A 780 ASN cc_start: 0.8566 (p0) cc_final: 0.8015 (p0) REVERT: A 791 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 759 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8546 (tm-30) REVERT: B 762 MET cc_start: 0.6855 (mtt) cc_final: 0.6565 (mtt) REVERT: B 780 ASN cc_start: 0.8224 (p0) cc_final: 0.7830 (p0) REVERT: B 786 MET cc_start: 0.8441 (tpp) cc_final: 0.7799 (ttt) REVERT: B 787 TYR cc_start: 0.8594 (m-10) cc_final: 0.8303 (m-80) REVERT: B 791 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 806 VAL cc_start: 0.9660 (OUTLIER) cc_final: 0.9303 (m) REVERT: C 759 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 762 MET cc_start: 0.7033 (mtt) cc_final: 0.6507 (mtt) REVERT: C 786 MET cc_start: 0.8142 (tpp) cc_final: 0.7635 (tpp) REVERT: C 787 TYR cc_start: 0.8445 (m-10) cc_final: 0.8080 (m-80) REVERT: C 791 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8555 (p) REVERT: C 800 TYR cc_start: 0.8400 (t80) cc_final: 0.8141 (t80) REVERT: C 868 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7578 (mmt90) REVERT: D 759 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 762 MET cc_start: 0.7067 (mtt) cc_final: 0.6475 (mtt) REVERT: D 780 ASN cc_start: 0.9094 (p0) cc_final: 0.8757 (p0) REVERT: D 786 MET cc_start: 0.8291 (tpp) cc_final: 0.7925 (tpp) REVERT: D 787 TYR cc_start: 0.8377 (m-10) cc_final: 0.7857 (m-80) REVERT: D 791 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 824 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: D 825 MET cc_start: 0.8145 (mtp) cc_final: 0.7785 (mtp) REVERT: E 762 MET cc_start: 0.7253 (mtt) cc_final: 0.6833 (mtt) REVERT: E 787 TYR cc_start: 0.8514 (m-10) cc_final: 0.8211 (m-10) REVERT: E 791 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 800 TYR cc_start: 0.8598 (t80) cc_final: 0.8358 (t80) REVERT: E 806 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9204 (m) REVERT: E 824 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: F 762 MET cc_start: 0.6848 (mtt) cc_final: 0.6602 (mtt) REVERT: F 780 ASN cc_start: 0.8416 (p0) cc_final: 0.7942 (p0) REVERT: F 787 TYR cc_start: 0.8728 (m-10) cc_final: 0.8204 (m-10) REVERT: F 791 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8403 (p) REVERT: G 759 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8678 (tm-30) REVERT: G 762 MET cc_start: 0.7170 (mtt) cc_final: 0.6376 (mtt) REVERT: G 780 ASN cc_start: 0.8335 (p0) cc_final: 0.8092 (p0) REVERT: G 787 TYR cc_start: 0.8640 (m-10) cc_final: 0.8321 (m-10) REVERT: G 791 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8732 (p) REVERT: G 868 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7520 (mmt180) REVERT: H 790 PRO cc_start: 0.6800 (Cg_endo) cc_final: 0.6542 (Cg_exo) REVERT: H 791 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8231 (m) REVERT: H 807 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6905 (mm-30) REVERT: H 824 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: H 856 LYS cc_start: 0.8508 (tmmt) cc_final: 0.7903 (tmtt) REVERT: H 870 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9040 (tt) REVERT: I 762 MET cc_start: 0.6732 (mtt) cc_final: 0.6358 (mtt) REVERT: I 803 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7771 (mtpp) REVERT: I 824 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: I 852 ILE cc_start: 0.8398 (pt) cc_final: 0.8176 (tp) REVERT: I 856 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8103 (tmtt) REVERT: I 870 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9027 (tt) REVERT: J 762 MET cc_start: 0.7206 (mtt) cc_final: 0.6850 (mtt) REVERT: J 786 MET cc_start: 0.8131 (tpp) cc_final: 0.7846 (mmm) REVERT: J 807 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6581 (mm-30) REVERT: K 791 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (m) REVERT: L 783 ILE cc_start: 0.9444 (mt) cc_final: 0.8905 (mt) REVERT: L 786 MET cc_start: 0.7983 (tpp) cc_final: 0.7535 (mmm) REVERT: L 824 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: L 856 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7338 (tmtt) REVERT: M 762 MET cc_start: 0.7227 (mtt) cc_final: 0.6844 (mtt) REVERT: M 783 ILE cc_start: 0.9622 (mt) cc_final: 0.8748 (mp) REVERT: M 786 MET cc_start: 0.8053 (tpp) cc_final: 0.7614 (mmm) REVERT: M 806 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8883 (t) REVERT: M 807 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6310 (mm-30) REVERT: M 852 ILE cc_start: 0.8282 (pt) cc_final: 0.7923 (tp) REVERT: N 762 MET cc_start: 0.7389 (mtt) cc_final: 0.7166 (mtt) REVERT: N 806 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8766 (t) REVERT: N 807 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6162 (mm-30) REVERT: N 824 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: N 856 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7896 (ttpp) outliers start: 140 outliers final: 25 residues processed: 589 average time/residue: 0.1116 time to fit residues: 94.4407 Evaluate side-chains 373 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 ASN ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069115 restraints weight = 52668.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070830 restraints weight = 29109.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071986 restraints weight = 18022.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072762 restraints weight = 12098.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073342 restraints weight = 8507.715| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13538 Z= 0.177 Angle : 0.730 6.333 18298 Z= 0.385 Chirality : 0.043 0.158 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.880 24.244 1820 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % 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: -5.53 (0.14), residues: 1582 helix: -4.34 (0.23), residues: 168 sheet: -2.03 (0.38), residues: 168 loop : -4.23 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 859 TYR 0.023 0.002 TYR L 855 PHE 0.011 0.001 PHE B 774 HIS 0.009 0.004 HIS M 765 Details of bonding type rmsd covalent geometry : bond 0.00401 (13538) covalent geometry : angle 0.72954 (18298) hydrogen bonds : bond 0.05016 ( 280) hydrogen bonds : angle 10.15933 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.545 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: A 759 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 780 ASN cc_start: 0.7759 (p0) cc_final: 0.7218 (p0) REVERT: A 800 TYR cc_start: 0.7793 (t80) cc_final: 0.7335 (t80) REVERT: B 759 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8226 (pm20) REVERT: B 780 ASN cc_start: 0.7872 (p0) cc_final: 0.7429 (p0) REVERT: B 786 MET cc_start: 0.8234 (tpp) cc_final: 0.7021 (ttt) REVERT: C 762 MET cc_start: 0.6136 (mtt) cc_final: 0.5370 (mtt) REVERT: C 791 THR cc_start: 0.8614 (p) cc_final: 0.8348 (p) REVERT: D 759 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 762 MET cc_start: 0.6197 (mtt) cc_final: 0.5480 (mtt) REVERT: D 780 ASN cc_start: 0.8115 (p0) cc_final: 0.7848 (p0) REVERT: D 791 THR cc_start: 0.8208 (p) cc_final: 0.7984 (p) REVERT: D 817 ASP cc_start: 0.8110 (t70) cc_final: 0.7862 (t0) REVERT: E 762 MET cc_start: 0.6831 (mtt) cc_final: 0.6560 (mtt) REVERT: E 786 MET cc_start: 0.8134 (tpp) cc_final: 0.7909 (tpp) REVERT: F 780 ASN cc_start: 0.7713 (p0) cc_final: 0.7385 (p0) REVERT: F 791 THR cc_start: 0.8371 (p) cc_final: 0.8151 (p) REVERT: G 759 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8444 (tm-30) REVERT: G 762 MET cc_start: 0.5949 (mtt) cc_final: 0.5524 (mtt) REVERT: G 780 ASN cc_start: 0.7876 (p0) cc_final: 0.7324 (p0) REVERT: G 791 THR cc_start: 0.8629 (p) cc_final: 0.8358 (p) REVERT: G 803 LYS cc_start: 0.8858 (mttt) cc_final: 0.8593 (mttm) REVERT: H 771 ASP cc_start: 0.8576 (t0) cc_final: 0.7440 (p0) REVERT: H 824 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7098 (tm-30) REVERT: I 762 MET cc_start: 0.6211 (mtt) cc_final: 0.5793 (mtt) REVERT: I 771 ASP cc_start: 0.8449 (t0) cc_final: 0.7359 (p0) REVERT: I 807 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7061 (mm-30) REVERT: I 856 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8386 (tttp) REVERT: I 860 ILE cc_start: 0.7943 (mm) cc_final: 0.7633 (mp) REVERT: J 762 MET cc_start: 0.6552 (mtt) cc_final: 0.5950 (mtt) REVERT: J 807 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7011 (mm-30) REVERT: J 870 LEU cc_start: 0.8936 (tt) cc_final: 0.8626 (tt) REVERT: K 771 ASP cc_start: 0.8738 (t0) cc_final: 0.7687 (p0) REVERT: K 772 LEU cc_start: 0.9193 (mp) cc_final: 0.8897 (mp) REVERT: L 786 MET cc_start: 0.8501 (tpp) cc_final: 0.8104 (mmm) REVERT: L 807 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7068 (mm-30) REVERT: L 870 LEU cc_start: 0.9300 (tt) cc_final: 0.8975 (tt) REVERT: M 771 ASP cc_start: 0.8814 (t0) cc_final: 0.7636 (p0) REVERT: M 807 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7084 (mm-30) REVERT: M 825 MET cc_start: 0.7903 (pmm) cc_final: 0.7644 (ptp) REVERT: N 762 MET cc_start: 0.6984 (mtt) cc_final: 0.6510 (mtt) REVERT: N 771 ASP cc_start: 0.8691 (t0) cc_final: 0.7560 (p0) REVERT: N 807 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6483 (mm-30) REVERT: N 825 MET cc_start: 0.8134 (ptp) cc_final: 0.7933 (ptp) REVERT: N 829 LEU cc_start: 0.9192 (tp) cc_final: 0.8989 (tp) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.1084 time to fit residues: 69.8031 Evaluate side-chains 321 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 851 ASN ** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065515 restraints weight = 53242.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.067205 restraints weight = 29405.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.068341 restraints weight = 18365.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069116 restraints weight = 12306.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069687 restraints weight = 8671.760| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13538 Z= 0.220 Angle : 0.761 10.143 18298 Z= 0.400 Chirality : 0.043 0.135 1918 Planarity : 0.007 0.072 2394 Dihedral : 6.774 22.257 1820 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.75 % Favored : 83.25 % Rotamer: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % 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: -5.41 (0.15), residues: 1582 helix: -4.21 (0.24), residues: 168 sheet: -1.70 (0.40), residues: 168 loop : -4.20 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 868 TYR 0.020 0.002 TYR K 855 PHE 0.014 0.002 PHE D 774 HIS 0.009 0.003 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00498 (13538) covalent geometry : angle 0.76133 (18298) hydrogen bonds : bond 0.05252 ( 280) hydrogen bonds : angle 10.02865 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 395 time to evaluate : 0.427 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: A 780 ASN cc_start: 0.8020 (p0) cc_final: 0.7564 (p0) REVERT: A 824 GLU cc_start: 0.8959 (tp30) cc_final: 0.8232 (tm-30) REVERT: A 861 TYR cc_start: 0.6137 (t80) cc_final: 0.5901 (t80) REVERT: B 780 ASN cc_start: 0.7898 (p0) cc_final: 0.7445 (p0) REVERT: B 786 MET cc_start: 0.8315 (tpp) cc_final: 0.7557 (ttt) REVERT: C 762 MET cc_start: 0.5933 (mtt) cc_final: 0.5210 (mtt) REVERT: C 786 MET cc_start: 0.8215 (tpp) cc_final: 0.8000 (tpp) REVERT: C 791 THR cc_start: 0.8682 (p) cc_final: 0.8281 (p) REVERT: D 759 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 762 MET cc_start: 0.6517 (mtt) cc_final: 0.5839 (mtt) REVERT: D 780 ASN cc_start: 0.8220 (p0) cc_final: 0.7966 (p0) REVERT: D 791 THR cc_start: 0.8464 (p) cc_final: 0.8205 (p) REVERT: D 800 TYR cc_start: 0.7787 (t80) cc_final: 0.7572 (t80) REVERT: D 825 MET cc_start: 0.7001 (tpt) cc_final: 0.6397 (tpp) REVERT: D 851 ASN cc_start: 0.7741 (t0) cc_final: 0.7472 (t0) REVERT: E 786 MET cc_start: 0.7950 (tpp) cc_final: 0.7660 (tpp) REVERT: E 824 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7823 (tm-30) REVERT: F 780 ASN cc_start: 0.8090 (p0) cc_final: 0.7766 (p0) REVERT: F 787 TYR cc_start: 0.8751 (m-80) cc_final: 0.8496 (m-80) REVERT: F 791 THR cc_start: 0.8458 (p) cc_final: 0.8222 (p) REVERT: G 759 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8358 (tm-30) REVERT: G 762 MET cc_start: 0.6180 (mtt) cc_final: 0.5544 (mtt) REVERT: G 780 ASN cc_start: 0.7989 (p0) cc_final: 0.7408 (p0) REVERT: G 803 LYS cc_start: 0.8920 (mttt) cc_final: 0.8634 (mttm) REVERT: H 771 ASP cc_start: 0.8701 (t0) cc_final: 0.7258 (p0) REVERT: H 772 LEU cc_start: 0.9247 (mp) cc_final: 0.8982 (mp) REVERT: I 762 MET cc_start: 0.6614 (mtt) cc_final: 0.6210 (mtt) REVERT: I 807 GLU cc_start: 0.7696 (mt-10) cc_final: 0.6790 (tm-30) REVERT: I 824 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8081 (tm-30) REVERT: I 856 LYS cc_start: 0.8774 (tmmt) cc_final: 0.8385 (tttp) REVERT: J 762 MET cc_start: 0.6933 (mtt) cc_final: 0.6519 (mtt) REVERT: J 807 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7093 (mm-30) REVERT: J 844 SER cc_start: 0.9159 (p) cc_final: 0.8949 (p) REVERT: J 870 LEU cc_start: 0.8864 (tt) cc_final: 0.8603 (tt) REVERT: K 771 ASP cc_start: 0.8857 (t0) cc_final: 0.7629 (p0) REVERT: K 772 LEU cc_start: 0.9252 (mp) cc_final: 0.8880 (mp) REVERT: L 771 ASP cc_start: 0.8634 (t70) cc_final: 0.7705 (p0) REVERT: L 772 LEU cc_start: 0.9351 (mp) cc_final: 0.9111 (mp) REVERT: L 786 MET cc_start: 0.8252 (tpp) cc_final: 0.8010 (mmm) REVERT: L 807 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7104 (mm-30) REVERT: L 844 SER cc_start: 0.9196 (p) cc_final: 0.8955 (p) REVERT: M 771 ASP cc_start: 0.8961 (t0) cc_final: 0.7864 (p0) REVERT: M 786 MET cc_start: 0.8861 (tpp) cc_final: 0.8611 (tpp) REVERT: M 807 GLU cc_start: 0.7660 (mt-10) cc_final: 0.6953 (mm-30) REVERT: N 762 MET cc_start: 0.6925 (mtt) cc_final: 0.6510 (mtt) REVERT: N 771 ASP cc_start: 0.8708 (t0) cc_final: 0.7296 (p0) REVERT: N 807 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6785 (tm-30) REVERT: N 817 ASP cc_start: 0.8696 (t0) cc_final: 0.8453 (t0) outliers start: 3 outliers final: 0 residues processed: 398 average time/residue: 0.1046 time to fit residues: 61.1185 Evaluate side-chains 307 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067374 restraints weight = 52194.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069112 restraints weight = 28630.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070270 restraints weight = 17663.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071055 restraints weight = 11753.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071522 restraints weight = 8241.661| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13538 Z= 0.179 Angle : 0.733 7.665 18298 Z= 0.381 Chirality : 0.044 0.144 1918 Planarity : 0.006 0.067 2394 Dihedral : 6.547 24.125 1820 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % 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: -5.54 (0.16), residues: 1582 helix: -3.90 (0.26), residues: 168 sheet: -3.24 (0.26), residues: 308 loop : -4.09 (0.13), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 868 TYR 0.015 0.001 TYR K 855 PHE 0.011 0.001 PHE J 774 HIS 0.007 0.003 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00409 (13538) covalent geometry : angle 0.73331 (18298) hydrogen bonds : bond 0.04641 ( 280) hydrogen bonds : angle 9.65640 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 0.530 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: A 780 ASN cc_start: 0.8032 (p0) cc_final: 0.7537 (p0) REVERT: A 824 GLU cc_start: 0.8866 (tp30) cc_final: 0.8320 (tm-30) REVERT: B 780 ASN cc_start: 0.7835 (p0) cc_final: 0.7455 (p0) REVERT: B 786 MET cc_start: 0.8333 (tpp) cc_final: 0.7418 (ttt) REVERT: B 787 TYR cc_start: 0.8572 (m-10) cc_final: 0.8240 (m-80) REVERT: B 803 LYS cc_start: 0.8975 (mttt) cc_final: 0.8728 (mttm) REVERT: B 824 GLU cc_start: 0.8751 (tp30) cc_final: 0.8097 (tm-30) REVERT: B 829 LEU cc_start: 0.9410 (mt) cc_final: 0.9095 (mt) REVERT: C 762 MET cc_start: 0.6333 (mtt) cc_final: 0.5706 (mtt) REVERT: C 786 MET cc_start: 0.8286 (tpp) cc_final: 0.8069 (tpp) REVERT: C 791 THR cc_start: 0.8444 (p) cc_final: 0.8212 (p) REVERT: C 856 LYS cc_start: 0.8841 (ttpp) cc_final: 0.8632 (ttpp) REVERT: C 866 ASP cc_start: 0.8755 (m-30) cc_final: 0.8550 (m-30) REVERT: D 759 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 762 MET cc_start: 0.6404 (mtt) cc_final: 0.5707 (mtt) REVERT: D 780 ASN cc_start: 0.8068 (p0) cc_final: 0.7800 (p0) REVERT: D 786 MET cc_start: 0.8586 (tpp) cc_final: 0.8264 (tpt) REVERT: D 791 THR cc_start: 0.8466 (p) cc_final: 0.8226 (p) REVERT: D 800 TYR cc_start: 0.7883 (t80) cc_final: 0.7656 (t80) REVERT: D 825 MET cc_start: 0.7489 (tpt) cc_final: 0.6381 (tpt) REVERT: E 780 ASN cc_start: 0.8024 (p0) cc_final: 0.7672 (p0) REVERT: E 786 MET cc_start: 0.8017 (tpp) cc_final: 0.7716 (ttt) REVERT: E 870 LEU cc_start: 0.9652 (tp) cc_final: 0.9445 (tt) REVERT: F 791 THR cc_start: 0.8357 (p) cc_final: 0.8125 (p) REVERT: G 759 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8452 (tm-30) REVERT: G 762 MET cc_start: 0.5941 (mtt) cc_final: 0.5372 (mtt) REVERT: G 780 ASN cc_start: 0.7935 (p0) cc_final: 0.7236 (p0) REVERT: G 803 LYS cc_start: 0.8950 (mttt) cc_final: 0.8606 (mttm) REVERT: H 771 ASP cc_start: 0.8689 (t0) cc_final: 0.7261 (p0) REVERT: H 772 LEU cc_start: 0.9254 (mp) cc_final: 0.8976 (mp) REVERT: I 762 MET cc_start: 0.6596 (mtt) cc_final: 0.6372 (mtt) REVERT: I 807 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6628 (tm-30) REVERT: I 824 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8140 (tm-30) REVERT: I 856 LYS cc_start: 0.8715 (tmmt) cc_final: 0.8181 (tttp) REVERT: I 869 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6133 (tm-30) REVERT: J 762 MET cc_start: 0.6920 (mtt) cc_final: 0.6557 (mtt) REVERT: J 807 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6786 (tm-30) REVERT: J 824 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8153 (tm-30) REVERT: J 844 SER cc_start: 0.9118 (p) cc_final: 0.8886 (p) REVERT: J 870 LEU cc_start: 0.8922 (tt) cc_final: 0.8662 (tt) REVERT: K 771 ASP cc_start: 0.8830 (t0) cc_final: 0.7597 (p0) REVERT: K 772 LEU cc_start: 0.9242 (mp) cc_final: 0.8832 (mp) REVERT: L 771 ASP cc_start: 0.8725 (t70) cc_final: 0.7995 (p0) REVERT: L 786 MET cc_start: 0.8239 (tpp) cc_final: 0.7968 (mmm) REVERT: L 807 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7182 (mm-30) REVERT: L 824 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8170 (tm-30) REVERT: M 771 ASP cc_start: 0.8956 (t0) cc_final: 0.7912 (p0) REVERT: M 786 MET cc_start: 0.8871 (tpp) cc_final: 0.8505 (tpp) REVERT: M 807 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6875 (tm-30) REVERT: N 762 MET cc_start: 0.6872 (mtt) cc_final: 0.6426 (mtt) REVERT: N 771 ASP cc_start: 0.8748 (t0) cc_final: 0.7211 (p0) REVERT: N 807 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6821 (tm-30) REVERT: N 817 ASP cc_start: 0.8789 (t0) cc_final: 0.8443 (t0) outliers start: 2 outliers final: 0 residues processed: 412 average time/residue: 0.1117 time to fit residues: 65.6182 Evaluate side-chains 310 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 792 GLN M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068354 restraints weight = 51959.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070089 restraints weight = 28787.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071265 restraints weight = 17944.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072079 restraints weight = 12037.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072657 restraints weight = 8558.757| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13538 Z= 0.151 Angle : 0.706 7.839 18298 Z= 0.366 Chirality : 0.043 0.148 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.292 22.439 1820 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.66 % Favored : 85.34 % Rotamer: Outliers : 0.21 % Allowed : 2.45 % Favored : 97.34 % 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: -5.41 (0.16), residues: 1582 helix: -3.75 (0.28), residues: 168 sheet: -3.18 (0.26), residues: 308 loop : -3.99 (0.14), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 868 TYR 0.017 0.001 TYR D 861 PHE 0.008 0.001 PHE N 774 HIS 0.008 0.003 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00348 (13538) covalent geometry : angle 0.70613 (18298) hydrogen bonds : bond 0.04340 ( 280) hydrogen bonds : angle 9.29799 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 0.519 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: A 780 ASN cc_start: 0.8060 (p0) cc_final: 0.7560 (p0) REVERT: A 824 GLU cc_start: 0.8919 (tp30) cc_final: 0.8564 (tp30) REVERT: A 825 MET cc_start: 0.7374 (mtt) cc_final: 0.7142 (mtp) REVERT: A 866 ASP cc_start: 0.8735 (m-30) cc_final: 0.8042 (t0) REVERT: B 780 ASN cc_start: 0.7789 (p0) cc_final: 0.7435 (p0) REVERT: B 786 MET cc_start: 0.8221 (tpp) cc_final: 0.7315 (ttt) REVERT: B 803 LYS cc_start: 0.9026 (mttt) cc_final: 0.8615 (mttm) REVERT: B 824 GLU cc_start: 0.8820 (tp30) cc_final: 0.8247 (tm-30) REVERT: B 829 LEU cc_start: 0.9379 (mt) cc_final: 0.9094 (mt) REVERT: B 860 ILE cc_start: 0.8131 (mm) cc_final: 0.7930 (mp) REVERT: B 866 ASP cc_start: 0.8776 (m-30) cc_final: 0.8439 (t0) REVERT: C 762 MET cc_start: 0.6555 (mtt) cc_final: 0.5830 (mtt) REVERT: C 786 MET cc_start: 0.8261 (tpp) cc_final: 0.8026 (tpp) REVERT: C 791 THR cc_start: 0.8486 (p) cc_final: 0.8244 (p) REVERT: D 762 MET cc_start: 0.6308 (mtt) cc_final: 0.5636 (mtt) REVERT: D 780 ASN cc_start: 0.8043 (p0) cc_final: 0.7708 (p0) REVERT: D 786 MET cc_start: 0.8643 (tpp) cc_final: 0.8319 (tpt) REVERT: D 791 THR cc_start: 0.8453 (p) cc_final: 0.8178 (p) REVERT: D 800 TYR cc_start: 0.7889 (t80) cc_final: 0.7670 (t80) REVERT: D 825 MET cc_start: 0.7081 (tpt) cc_final: 0.6086 (tpt) REVERT: E 780 ASN cc_start: 0.8019 (p0) cc_final: 0.7715 (p0) REVERT: E 786 MET cc_start: 0.8107 (tpp) cc_final: 0.7620 (ttt) REVERT: E 803 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8539 (mttm) REVERT: F 860 ILE cc_start: 0.8409 (mm) cc_final: 0.8194 (mp) REVERT: G 759 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8583 (tm-30) REVERT: G 762 MET cc_start: 0.6104 (mtt) cc_final: 0.5523 (mtt) REVERT: G 780 ASN cc_start: 0.8027 (p0) cc_final: 0.7319 (p0) REVERT: G 803 LYS cc_start: 0.8953 (mttt) cc_final: 0.8588 (mttm) REVERT: G 868 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.6900 (tpt-90) REVERT: H 771 ASP cc_start: 0.8708 (t0) cc_final: 0.7241 (p0) REVERT: I 762 MET cc_start: 0.6458 (mtt) cc_final: 0.6157 (mtt) REVERT: I 807 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6681 (tm-30) REVERT: I 824 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8200 (tm-30) REVERT: J 762 MET cc_start: 0.6952 (mtt) cc_final: 0.6594 (mtt) REVERT: J 807 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6757 (tm-30) REVERT: J 844 SER cc_start: 0.9105 (p) cc_final: 0.8872 (p) REVERT: K 771 ASP cc_start: 0.8725 (t0) cc_final: 0.7603 (p0) REVERT: K 859 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6562 (mmm-85) REVERT: L 786 MET cc_start: 0.8327 (tpp) cc_final: 0.7993 (mmm) REVERT: L 807 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6345 (tm-30) REVERT: L 817 ASP cc_start: 0.8820 (t0) cc_final: 0.8613 (t0) REVERT: L 824 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8250 (tm-30) REVERT: L 844 SER cc_start: 0.9275 (p) cc_final: 0.9051 (p) REVERT: M 786 MET cc_start: 0.8834 (tpp) cc_final: 0.8604 (tpp) REVERT: M 807 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6809 (tm-30) REVERT: M 824 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7615 (tm-30) REVERT: N 762 MET cc_start: 0.7012 (mtt) cc_final: 0.6509 (mtt) REVERT: N 771 ASP cc_start: 0.8763 (t0) cc_final: 0.7198 (p0) REVERT: N 807 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6887 (tm-30) REVERT: N 817 ASP cc_start: 0.8768 (t0) cc_final: 0.8363 (t0) outliers start: 3 outliers final: 0 residues processed: 412 average time/residue: 0.1149 time to fit residues: 66.9053 Evaluate side-chains 330 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.075326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069050 restraints weight = 52251.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070757 restraints weight = 28893.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071925 restraints weight = 18089.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.072749 restraints weight = 12155.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.073314 restraints weight = 8543.127| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13538 Z= 0.143 Angle : 0.717 8.289 18298 Z= 0.367 Chirality : 0.043 0.207 1918 Planarity : 0.006 0.067 2394 Dihedral : 6.176 23.707 1820 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.54 % Favored : 85.46 % Rotamer: Outliers : 0.14 % Allowed : 1.26 % Favored : 98.60 % 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: -4.98 (0.16), residues: 1582 helix: -3.61 (0.29), residues: 168 sheet: -1.54 (0.40), residues: 168 loop : -3.91 (0.13), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 859 TYR 0.019 0.001 TYR G 800 PHE 0.007 0.001 PHE J 774 HIS 0.009 0.003 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00331 (13538) covalent geometry : angle 0.71677 (18298) hydrogen bonds : bond 0.04322 ( 280) hydrogen bonds : angle 9.07105 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.386 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: A 780 ASN cc_start: 0.8117 (p0) cc_final: 0.7628 (p0) REVERT: A 816 LYS cc_start: 0.8983 (ptmt) cc_final: 0.8659 (ptmt) REVERT: A 824 GLU cc_start: 0.8717 (tp30) cc_final: 0.8437 (tm-30) REVERT: A 825 MET cc_start: 0.7328 (mtt) cc_final: 0.7088 (mtt) REVERT: A 866 ASP cc_start: 0.8382 (m-30) cc_final: 0.8178 (t0) REVERT: B 780 ASN cc_start: 0.7770 (p0) cc_final: 0.7425 (p0) REVERT: B 786 MET cc_start: 0.8305 (tpp) cc_final: 0.7549 (ttt) REVERT: B 803 LYS cc_start: 0.9062 (mttt) cc_final: 0.8712 (mttm) REVERT: B 829 LEU cc_start: 0.9323 (mt) cc_final: 0.9055 (mt) REVERT: B 866 ASP cc_start: 0.8804 (m-30) cc_final: 0.8543 (t0) REVERT: C 762 MET cc_start: 0.6596 (mtt) cc_final: 0.5784 (mtt) REVERT: C 786 MET cc_start: 0.8288 (tpp) cc_final: 0.8007 (tpp) REVERT: C 791 THR cc_start: 0.8497 (p) cc_final: 0.8222 (p) REVERT: D 762 MET cc_start: 0.6371 (mtt) cc_final: 0.5702 (mtt) REVERT: D 780 ASN cc_start: 0.7993 (p0) cc_final: 0.7716 (p0) REVERT: D 786 MET cc_start: 0.8611 (tpp) cc_final: 0.8297 (tpt) REVERT: D 791 THR cc_start: 0.8450 (p) cc_final: 0.8164 (p) REVERT: D 825 MET cc_start: 0.7064 (tpt) cc_final: 0.6144 (tpt) REVERT: E 786 MET cc_start: 0.7918 (tpp) cc_final: 0.7641 (ttt) REVERT: E 803 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8354 (mttm) REVERT: E 866 ASP cc_start: 0.8420 (m-30) cc_final: 0.8113 (t0) REVERT: G 759 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8578 (tm-30) REVERT: G 762 MET cc_start: 0.6087 (mtt) cc_final: 0.5436 (mtt) REVERT: G 780 ASN cc_start: 0.7902 (p0) cc_final: 0.7602 (p0) REVERT: G 803 LYS cc_start: 0.8967 (mttt) cc_final: 0.8557 (mttm) REVERT: H 771 ASP cc_start: 0.8727 (t0) cc_final: 0.7256 (p0) REVERT: H 772 LEU cc_start: 0.9453 (mt) cc_final: 0.9052 (mp) REVERT: I 762 MET cc_start: 0.6466 (mtt) cc_final: 0.6138 (mtt) REVERT: I 807 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6720 (tm-30) REVERT: I 824 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8251 (tm-30) REVERT: J 762 MET cc_start: 0.6910 (mtt) cc_final: 0.6526 (mtt) REVERT: J 844 SER cc_start: 0.9068 (p) cc_final: 0.8811 (p) REVERT: K 771 ASP cc_start: 0.8725 (t0) cc_final: 0.7661 (p0) REVERT: K 791 THR cc_start: 0.8015 (m) cc_final: 0.7553 (p) REVERT: K 859 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.6726 (mmm-85) REVERT: L 771 ASP cc_start: 0.8814 (t0) cc_final: 0.7706 (p0) REVERT: L 772 LEU cc_start: 0.9300 (mp) cc_final: 0.8989 (mp) REVERT: L 807 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7075 (mm-30) REVERT: L 824 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8234 (tm-30) REVERT: L 844 SER cc_start: 0.9132 (p) cc_final: 0.8908 (p) REVERT: M 771 ASP cc_start: 0.8678 (t70) cc_final: 0.7876 (p0) REVERT: M 786 MET cc_start: 0.8800 (tpp) cc_final: 0.8504 (tpp) REVERT: M 807 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6924 (tm-30) REVERT: M 824 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7834 (tm-30) REVERT: N 762 MET cc_start: 0.6956 (mtt) cc_final: 0.6322 (mtt) REVERT: N 807 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6884 (tm-30) REVERT: N 817 ASP cc_start: 0.8769 (t0) cc_final: 0.8373 (t0) outliers start: 2 outliers final: 0 residues processed: 401 average time/residue: 0.1153 time to fit residues: 65.9054 Evaluate side-chains 323 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 765 HIS ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 765 HIS ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066291 restraints weight = 52546.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067941 restraints weight = 28980.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069071 restraints weight = 18092.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069838 restraints weight = 12116.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070383 restraints weight = 8508.884| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13538 Z= 0.216 Angle : 0.787 8.627 18298 Z= 0.409 Chirality : 0.045 0.184 1918 Planarity : 0.007 0.068 2394 Dihedral : 6.464 21.996 1820 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.39 % 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: -4.87 (0.17), residues: 1582 helix: -3.36 (0.32), residues: 168 sheet: -1.56 (0.39), residues: 168 loop : -3.83 (0.13), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 868 TYR 0.023 0.002 TYR D 861 PHE 0.016 0.002 PHE J 774 HIS 0.009 0.003 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00490 (13538) covalent geometry : angle 0.78656 (18298) hydrogen bonds : bond 0.05190 ( 280) hydrogen bonds : angle 9.10263 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.470 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: A 780 ASN cc_start: 0.8342 (p0) cc_final: 0.8097 (p0) REVERT: A 824 GLU cc_start: 0.8797 (tp30) cc_final: 0.8496 (tm-30) REVERT: A 825 MET cc_start: 0.7547 (mtt) cc_final: 0.7255 (mtt) REVERT: A 856 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8591 (tptp) REVERT: A 866 ASP cc_start: 0.8411 (m-30) cc_final: 0.8001 (t0) REVERT: A 868 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7746 (mmm-85) REVERT: A 870 LEU cc_start: 0.9541 (tp) cc_final: 0.9330 (tp) REVERT: B 759 GLN cc_start: 0.8598 (pm20) cc_final: 0.8397 (pm20) REVERT: B 762 MET cc_start: 0.7792 (mpp) cc_final: 0.7442 (mpp) REVERT: B 780 ASN cc_start: 0.8236 (p0) cc_final: 0.7938 (p0) REVERT: B 786 MET cc_start: 0.8323 (tpp) cc_final: 0.7687 (ttt) REVERT: B 803 LYS cc_start: 0.9062 (mttt) cc_final: 0.8741 (mttm) REVERT: B 824 GLU cc_start: 0.9020 (tp30) cc_final: 0.8534 (tm-30) REVERT: B 829 LEU cc_start: 0.9402 (mt) cc_final: 0.9110 (mt) REVERT: B 866 ASP cc_start: 0.8835 (m-30) cc_final: 0.8442 (t0) REVERT: B 870 LEU cc_start: 0.9784 (tp) cc_final: 0.9542 (tp) REVERT: C 762 MET cc_start: 0.6850 (mtt) cc_final: 0.5919 (mtt) REVERT: C 786 MET cc_start: 0.8372 (tpp) cc_final: 0.8050 (tpp) REVERT: C 791 THR cc_start: 0.8459 (p) cc_final: 0.8250 (p) REVERT: C 825 MET cc_start: 0.8332 (tpt) cc_final: 0.7465 (tpt) REVERT: D 762 MET cc_start: 0.6573 (mtt) cc_final: 0.5820 (mtt) REVERT: D 780 ASN cc_start: 0.8381 (p0) cc_final: 0.7933 (p0) REVERT: D 786 MET cc_start: 0.8426 (tpp) cc_final: 0.7792 (tpt) REVERT: D 791 THR cc_start: 0.8571 (p) cc_final: 0.8288 (p) REVERT: D 825 MET cc_start: 0.7012 (tpt) cc_final: 0.6284 (tpt) REVERT: E 786 MET cc_start: 0.8152 (tpp) cc_final: 0.7812 (ttt) REVERT: E 787 TYR cc_start: 0.9112 (m-80) cc_final: 0.8662 (m-10) REVERT: E 803 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8245 (mttm) REVERT: E 866 ASP cc_start: 0.8678 (m-30) cc_final: 0.8235 (t70) REVERT: F 860 ILE cc_start: 0.8069 (mp) cc_final: 0.7845 (mp) REVERT: G 759 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8547 (tm-30) REVERT: G 762 MET cc_start: 0.6786 (mtt) cc_final: 0.5835 (mtt) REVERT: G 780 ASN cc_start: 0.8247 (p0) cc_final: 0.8001 (p0) REVERT: G 803 LYS cc_start: 0.8986 (mttt) cc_final: 0.8566 (mttm) REVERT: G 853 MET cc_start: 0.7772 (ppp) cc_final: 0.7443 (ppp) REVERT: G 868 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7243 (tpp80) REVERT: H 762 MET cc_start: 0.8116 (mtm) cc_final: 0.7895 (mtt) REVERT: H 771 ASP cc_start: 0.8845 (t0) cc_final: 0.7265 (p0) REVERT: H 772 LEU cc_start: 0.9547 (mt) cc_final: 0.9084 (mp) REVERT: I 762 MET cc_start: 0.6853 (mtt) cc_final: 0.6449 (mtt) REVERT: I 771 ASP cc_start: 0.8811 (t0) cc_final: 0.6979 (p0) REVERT: I 807 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6617 (tm-30) REVERT: I 824 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8219 (tm-30) REVERT: J 762 MET cc_start: 0.7105 (mtt) cc_final: 0.6556 (mtt) REVERT: J 844 SER cc_start: 0.9160 (p) cc_final: 0.8933 (p) REVERT: J 870 LEU cc_start: 0.8753 (tt) cc_final: 0.8515 (tt) REVERT: K 771 ASP cc_start: 0.8777 (t0) cc_final: 0.7396 (p0) REVERT: K 791 THR cc_start: 0.8159 (m) cc_final: 0.7702 (p) REVERT: L 824 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8313 (tm-30) REVERT: L 844 SER cc_start: 0.9271 (p) cc_final: 0.9029 (p) REVERT: M 771 ASP cc_start: 0.8661 (t70) cc_final: 0.7815 (p0) REVERT: M 807 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7153 (tm-30) REVERT: M 824 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8463 (tm-30) REVERT: N 762 MET cc_start: 0.6866 (mtt) cc_final: 0.6319 (mtt) REVERT: N 807 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6860 (tm-30) REVERT: N 817 ASP cc_start: 0.8796 (t0) cc_final: 0.8391 (t0) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.1124 time to fit residues: 63.1723 Evaluate side-chains 316 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 109 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.076727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070561 restraints weight = 51689.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072227 restraints weight = 29029.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073387 restraints weight = 18343.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074169 restraints weight = 12369.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074736 restraints weight = 8779.692| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13538 Z= 0.131 Angle : 0.732 8.740 18298 Z= 0.372 Chirality : 0.044 0.185 1918 Planarity : 0.006 0.064 2394 Dihedral : 6.096 23.091 1820 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 0.14 % Allowed : 0.77 % Favored : 99.09 % 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: -5.05 (0.17), residues: 1582 helix: -3.57 (0.30), residues: 168 sheet: -3.00 (0.26), residues: 308 loop : -3.69 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 859 TYR 0.020 0.001 TYR C 861 PHE 0.020 0.001 PHE B 788 HIS 0.013 0.003 HIS D 765 Details of bonding type rmsd covalent geometry : bond 0.00305 (13538) covalent geometry : angle 0.73204 (18298) hydrogen bonds : bond 0.04101 ( 280) hydrogen bonds : angle 8.90143 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 405 time to evaluate : 0.513 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: A 762 MET cc_start: 0.7394 (mtm) cc_final: 0.7173 (mtt) REVERT: A 780 ASN cc_start: 0.8124 (p0) cc_final: 0.7649 (p0) REVERT: A 861 TYR cc_start: 0.5927 (t80) cc_final: 0.5694 (t80) REVERT: A 868 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7697 (mmm-85) REVERT: B 780 ASN cc_start: 0.7901 (p0) cc_final: 0.7641 (p0) REVERT: B 786 MET cc_start: 0.7891 (tpp) cc_final: 0.7050 (ttt) REVERT: B 803 LYS cc_start: 0.9012 (mttt) cc_final: 0.8646 (mttm) REVERT: B 868 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7527 (mmm-85) REVERT: C 762 MET cc_start: 0.6382 (mtt) cc_final: 0.5532 (mtt) REVERT: C 786 MET cc_start: 0.8237 (tpp) cc_final: 0.8005 (tpp) REVERT: C 791 THR cc_start: 0.8392 (p) cc_final: 0.8100 (p) REVERT: D 762 MET cc_start: 0.6212 (mtt) cc_final: 0.5715 (mtt) REVERT: D 780 ASN cc_start: 0.8177 (p0) cc_final: 0.7790 (p0) REVERT: D 786 MET cc_start: 0.8216 (tpp) cc_final: 0.7608 (tpt) REVERT: D 791 THR cc_start: 0.8511 (p) cc_final: 0.8229 (p) REVERT: D 825 MET cc_start: 0.6871 (tpt) cc_final: 0.5647 (tpt) REVERT: E 780 ASN cc_start: 0.8039 (p0) cc_final: 0.7836 (p0) REVERT: E 786 MET cc_start: 0.7923 (tpp) cc_final: 0.7543 (ttt) REVERT: E 803 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8176 (mttm) REVERT: E 853 MET cc_start: 0.6763 (ppp) cc_final: 0.6559 (ppp) REVERT: E 870 LEU cc_start: 0.9588 (tp) cc_final: 0.9327 (tt) REVERT: F 787 TYR cc_start: 0.8783 (m-80) cc_final: 0.8136 (m-80) REVERT: F 824 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7896 (tm-30) REVERT: F 856 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8576 (tptp) REVERT: G 759 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8483 (tm-30) REVERT: G 762 MET cc_start: 0.6456 (mtt) cc_final: 0.5552 (mtt) REVERT: G 780 ASN cc_start: 0.7976 (p0) cc_final: 0.7756 (p0) REVERT: G 803 LYS cc_start: 0.8905 (mttt) cc_final: 0.8604 (mttm) REVERT: G 853 MET cc_start: 0.7852 (ppp) cc_final: 0.7408 (ppp) REVERT: G 868 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7279 (tpt-90) REVERT: H 771 ASP cc_start: 0.8613 (t0) cc_final: 0.7369 (p0) REVERT: H 772 LEU cc_start: 0.9449 (mt) cc_final: 0.9014 (mp) REVERT: I 762 MET cc_start: 0.6378 (mtt) cc_final: 0.6098 (mtt) REVERT: I 771 ASP cc_start: 0.8576 (t0) cc_final: 0.7097 (p0) REVERT: I 807 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6750 (tm-30) REVERT: I 824 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8247 (tm-30) REVERT: J 762 MET cc_start: 0.6772 (mtt) cc_final: 0.6335 (mtt) REVERT: J 807 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6535 (tm-30) REVERT: J 844 SER cc_start: 0.8953 (p) cc_final: 0.8715 (p) REVERT: K 771 ASP cc_start: 0.8540 (t0) cc_final: 0.7502 (p0) REVERT: K 791 THR cc_start: 0.7810 (m) cc_final: 0.7325 (p) REVERT: L 762 MET cc_start: 0.7887 (mtm) cc_final: 0.7522 (mtt) REVERT: L 822 ASP cc_start: 0.8450 (m-30) cc_final: 0.8201 (m-30) REVERT: L 824 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8361 (tm-30) REVERT: L 844 SER cc_start: 0.9076 (p) cc_final: 0.8808 (p) REVERT: M 771 ASP cc_start: 0.8622 (t70) cc_final: 0.7907 (p0) REVERT: M 807 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7326 (tm-30) REVERT: N 762 MET cc_start: 0.6581 (mtt) cc_final: 0.6048 (mtt) REVERT: N 786 MET cc_start: 0.9070 (tpp) cc_final: 0.8814 (tpp) REVERT: N 807 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6928 (tm-30) REVERT: N 817 ASP cc_start: 0.8723 (t0) cc_final: 0.8207 (t0) outliers start: 2 outliers final: 1 residues processed: 407 average time/residue: 0.1095 time to fit residues: 64.4317 Evaluate side-chains 335 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 794 ASN ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.072808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066620 restraints weight = 53117.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068295 restraints weight = 29630.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069436 restraints weight = 18563.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070228 restraints weight = 12540.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070777 restraints weight = 8877.140| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13538 Z= 0.210 Angle : 0.806 9.919 18298 Z= 0.416 Chirality : 0.046 0.176 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.326 22.559 1820 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.14 % Favored : 81.86 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % 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: -5.01 (0.17), residues: 1582 helix: -3.53 (0.31), residues: 168 sheet: -2.95 (0.26), residues: 308 loop : -3.67 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 868 TYR 0.031 0.002 TYR D 861 PHE 0.015 0.002 PHE J 774 HIS 0.011 0.003 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00479 (13538) covalent geometry : angle 0.80550 (18298) hydrogen bonds : bond 0.05139 ( 280) hydrogen bonds : angle 9.00740 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.488 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: A 780 ASN cc_start: 0.8289 (p0) cc_final: 0.7893 (p0) REVERT: A 786 MET cc_start: 0.8119 (tpp) cc_final: 0.7683 (ttt) REVERT: A 866 ASP cc_start: 0.8859 (t0) cc_final: 0.8510 (t0) REVERT: A 868 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7550 (mmm-85) REVERT: B 759 GLN cc_start: 0.8605 (pm20) cc_final: 0.8379 (pp30) REVERT: B 762 MET cc_start: 0.7662 (mpp) cc_final: 0.7306 (mpp) REVERT: B 780 ASN cc_start: 0.8115 (p0) cc_final: 0.7912 (p0) REVERT: B 786 MET cc_start: 0.8035 (tpp) cc_final: 0.7465 (ttt) REVERT: B 803 LYS cc_start: 0.8928 (mttt) cc_final: 0.8491 (mttm) REVERT: B 825 MET cc_start: 0.8314 (tpp) cc_final: 0.7899 (tpp) REVERT: B 829 LEU cc_start: 0.9360 (mt) cc_final: 0.9117 (mt) REVERT: B 868 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7918 (tpp80) REVERT: C 762 MET cc_start: 0.6687 (mtt) cc_final: 0.5762 (mtt) REVERT: C 791 THR cc_start: 0.8444 (p) cc_final: 0.8185 (p) REVERT: D 762 MET cc_start: 0.6451 (mtt) cc_final: 0.5818 (mtt) REVERT: D 780 ASN cc_start: 0.8276 (p0) cc_final: 0.7712 (p0) REVERT: D 786 MET cc_start: 0.8280 (tpp) cc_final: 0.7599 (tpt) REVERT: D 791 THR cc_start: 0.8603 (p) cc_final: 0.8321 (p) REVERT: D 825 MET cc_start: 0.6721 (tpt) cc_final: 0.5721 (tpt) REVERT: D 870 LEU cc_start: 0.9610 (tp) cc_final: 0.9377 (tt) REVERT: E 803 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8405 (mttm) REVERT: F 824 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7908 (tm-30) REVERT: F 870 LEU cc_start: 0.9584 (tp) cc_final: 0.9371 (tt) REVERT: G 759 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8465 (tm-30) REVERT: G 762 MET cc_start: 0.6691 (mtt) cc_final: 0.5700 (mtt) REVERT: G 780 ASN cc_start: 0.8222 (p0) cc_final: 0.8004 (p0) REVERT: G 803 LYS cc_start: 0.8969 (mttt) cc_final: 0.8635 (mttm) REVERT: G 868 ARG cc_start: 0.7988 (tpp-160) cc_final: 0.7085 (tpp80) REVERT: H 762 MET cc_start: 0.8111 (mtm) cc_final: 0.7869 (mtt) REVERT: H 771 ASP cc_start: 0.8739 (t0) cc_final: 0.7318 (p0) REVERT: I 762 MET cc_start: 0.6787 (mtt) cc_final: 0.6341 (mtt) REVERT: I 807 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6683 (tm-30) REVERT: I 824 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8371 (tm-30) REVERT: I 858 LEU cc_start: 0.8682 (tp) cc_final: 0.7637 (tt) REVERT: J 762 MET cc_start: 0.6950 (mtt) cc_final: 0.6425 (mtt) REVERT: J 844 SER cc_start: 0.9095 (p) cc_final: 0.8838 (p) REVERT: K 762 MET cc_start: 0.8032 (mtm) cc_final: 0.7827 (mtt) REVERT: K 771 ASP cc_start: 0.8653 (t0) cc_final: 0.7409 (p0) REVERT: K 791 THR cc_start: 0.8012 (m) cc_final: 0.7595 (p) REVERT: K 858 LEU cc_start: 0.8778 (tp) cc_final: 0.8132 (tt) REVERT: L 762 MET cc_start: 0.8102 (mtm) cc_final: 0.7715 (mtt) REVERT: L 824 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8359 (tm-30) REVERT: L 844 SER cc_start: 0.9232 (p) cc_final: 0.8971 (p) REVERT: M 807 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7416 (tm-30) REVERT: N 762 MET cc_start: 0.6780 (mtt) cc_final: 0.6211 (mtt) outliers start: 1 outliers final: 1 residues processed: 385 average time/residue: 0.1112 time to fit residues: 62.0492 Evaluate side-chains 318 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.072925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066787 restraints weight = 52792.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068443 restraints weight = 29317.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.069602 restraints weight = 18241.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070370 restraints weight = 12241.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070921 restraints weight = 8708.179| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13538 Z= 0.191 Angle : 0.803 9.791 18298 Z= 0.414 Chirality : 0.046 0.176 1918 Planarity : 0.006 0.065 2394 Dihedral : 6.416 23.039 1820 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -4.96 (0.17), residues: 1582 helix: -3.51 (0.31), residues: 168 sheet: -2.94 (0.26), residues: 308 loop : -3.63 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 859 TYR 0.034 0.001 TYR B 861 PHE 0.012 0.001 PHE J 774 HIS 0.008 0.003 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00437 (13538) covalent geometry : angle 0.80276 (18298) hydrogen bonds : bond 0.05107 ( 280) hydrogen bonds : angle 8.92725 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.502 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: A 780 ASN cc_start: 0.8338 (p0) cc_final: 0.8119 (p0) REVERT: A 861 TYR cc_start: 0.6132 (t80) cc_final: 0.5777 (t80) REVERT: A 866 ASP cc_start: 0.8886 (t0) cc_final: 0.8509 (t0) REVERT: A 868 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7546 (mmm-85) REVERT: B 759 GLN cc_start: 0.8561 (pm20) cc_final: 0.8327 (pp30) REVERT: B 762 MET cc_start: 0.7623 (mpp) cc_final: 0.7212 (mpp) REVERT: B 780 ASN cc_start: 0.7991 (p0) cc_final: 0.7749 (p0) REVERT: B 786 MET cc_start: 0.7993 (tpp) cc_final: 0.7523 (ttt) REVERT: B 803 LYS cc_start: 0.8931 (mttt) cc_final: 0.8500 (mttm) REVERT: B 825 MET cc_start: 0.8195 (tpp) cc_final: 0.7777 (tpp) REVERT: C 762 MET cc_start: 0.6644 (mtt) cc_final: 0.5711 (mtt) REVERT: C 791 THR cc_start: 0.8423 (p) cc_final: 0.8183 (p) REVERT: C 825 MET cc_start: 0.8515 (tpt) cc_final: 0.7812 (tpt) REVERT: C 829 LEU cc_start: 0.9461 (mt) cc_final: 0.9085 (mt) REVERT: D 762 MET cc_start: 0.6490 (mtt) cc_final: 0.5797 (mtt) REVERT: D 780 ASN cc_start: 0.8314 (p0) cc_final: 0.7722 (p0) REVERT: D 791 THR cc_start: 0.8538 (p) cc_final: 0.8241 (p) REVERT: D 825 MET cc_start: 0.6784 (tpt) cc_final: 0.5768 (tpt) REVERT: D 870 LEU cc_start: 0.9406 (tp) cc_final: 0.9137 (tp) REVERT: E 761 ILE cc_start: 0.8776 (mt) cc_final: 0.8539 (mm) REVERT: E 803 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8400 (mttm) REVERT: F 824 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8017 (tm-30) REVERT: F 870 LEU cc_start: 0.9564 (tp) cc_final: 0.9350 (tt) REVERT: G 759 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8523 (tm-30) REVERT: G 762 MET cc_start: 0.6667 (mtt) cc_final: 0.5658 (mtt) REVERT: G 803 LYS cc_start: 0.8958 (mttt) cc_final: 0.8553 (mttm) REVERT: G 853 MET cc_start: 0.7704 (ppp) cc_final: 0.7347 (ppp) REVERT: G 861 TYR cc_start: 0.6264 (t80) cc_final: 0.6017 (t80) REVERT: G 868 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7147 (tpt-90) REVERT: H 762 MET cc_start: 0.8263 (mtm) cc_final: 0.7862 (mtt) REVERT: H 771 ASP cc_start: 0.8603 (t0) cc_final: 0.7462 (p0) REVERT: H 772 LEU cc_start: 0.9393 (mt) cc_final: 0.9125 (mt) REVERT: I 762 MET cc_start: 0.6766 (mtt) cc_final: 0.6371 (mtt) REVERT: I 807 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6546 (tm-30) REVERT: I 824 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8470 (tm-30) REVERT: J 762 MET cc_start: 0.6973 (mtt) cc_final: 0.6393 (mtt) REVERT: J 783 ILE cc_start: 0.9629 (tt) cc_final: 0.9273 (mp) REVERT: J 844 SER cc_start: 0.9077 (p) cc_final: 0.8832 (p) REVERT: J 870 LEU cc_start: 0.8659 (tt) cc_final: 0.8449 (tt) REVERT: K 762 MET cc_start: 0.7996 (mtm) cc_final: 0.7754 (mtt) REVERT: K 771 ASP cc_start: 0.8762 (t0) cc_final: 0.7501 (p0) REVERT: K 791 THR cc_start: 0.7991 (m) cc_final: 0.7558 (p) REVERT: L 762 MET cc_start: 0.8062 (mtm) cc_final: 0.7637 (mtt) REVERT: L 824 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8357 (tm-30) REVERT: L 844 SER cc_start: 0.9225 (p) cc_final: 0.8954 (p) REVERT: L 859 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.7600 (mmt-90) REVERT: M 807 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7459 (tm-30) REVERT: N 762 MET cc_start: 0.6745 (mtt) cc_final: 0.6165 (mtt) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1120 time to fit residues: 63.0239 Evaluate side-chains 328 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 0.2980 chunk 101 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.075322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069098 restraints weight = 52238.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070804 restraints weight = 29057.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071922 restraints weight = 18134.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072720 restraints weight = 12247.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073292 restraints weight = 8717.747| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13538 Z= 0.140 Angle : 0.770 9.378 18298 Z= 0.392 Chirality : 0.045 0.161 1918 Planarity : 0.006 0.068 2394 Dihedral : 6.089 22.453 1820 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -4.90 (0.17), residues: 1582 helix: -3.66 (0.29), residues: 168 sheet: -2.93 (0.26), residues: 308 loop : -3.54 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 868 TYR 0.033 0.001 TYR D 861 PHE 0.009 0.001 PHE H 788 HIS 0.008 0.002 HIS E 765 Details of bonding type rmsd covalent geometry : bond 0.00324 (13538) covalent geometry : angle 0.77016 (18298) hydrogen bonds : bond 0.04601 ( 280) hydrogen bonds : angle 8.79346 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.12 seconds wall clock time: 33 minutes 34.78 seconds (2014.78 seconds total)