Starting phenix.real_space_refine on Thu Aug 6 04:12:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbn_16546/08_2026/8cbn_16546.cif" } resolution = 3.34 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= 0.024 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 15 5.16 5 C 7698 2.51 5 N 2540 2.21 5 O 3116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13669 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.42, per 1000 atoms: 0.18 Number of scatterers: 13669 At special positions: 0 Unit cell: (81.144, 139.104, 129.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 300 15.00 O 3116 8.00 N 2540 7.00 C 7698 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: 0.85 Conformation dependent library (CDL) restraints added in 539.7 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 58.1% alpha, 5.1% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.790A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.765A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.586A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.956A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.555A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.684A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.629A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 87 removed outlier: 5.136A pdb=" N ASP L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 86 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.151A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.434A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.168A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.622A pdb=" N PHE K 43 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.623A pdb=" N PHE L 43 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA L 13 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA L 23 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 11 " --> pdb=" O ALA L 23 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 4911 1.45 - 1.57: 6654 1.57 - 1.69: 598 1.69 - 1.81: 30 Bond restraints: 14550 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.40e+01 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" C3' DG I -7 " pdb=" O3' DG I -7 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 14545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 19332 1.59 - 3.18: 1525 3.18 - 4.78: 55 4.78 - 6.37: 16 6.37 - 7.96: 7 Bond angle restraints: 20935 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 119.70 125.90 -6.20 1.20e+00 6.94e-01 2.67e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 119.70 125.02 -5.32 1.20e+00 6.94e-01 1.96e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 119.70 124.97 -5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" N3 DT I 55 " pdb=" C4 DT I 55 " pdb=" O4 DT I 55 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 20930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 6580 34.29 - 68.57: 1388 68.57 - 102.86: 15 102.86 - 137.15: 2 137.15 - 171.44: 1 Dihedral angle restraints: 7986 sinusoidal: 5267 harmonic: 2719 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.56 171.44 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1282 0.041 - 0.083: 786 0.083 - 0.124: 219 0.124 - 0.166: 56 0.166 - 0.207: 4 Chirality restraints: 2347 Sorted by residual: chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' DT I 34 " pdb=" C4' DT I 34 " pdb=" O3' DT I 34 " pdb=" C2' DT I 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 2344 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 66 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO G 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO C 80 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.037 5.00e-02 4.00e+02 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.68: 2 1.68 - 2.49: 54 2.49 - 3.29: 12951 3.29 - 4.10: 39079 4.10 - 4.90: 66074 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118160 Sorted by model distance: nonbonded pdb=" OP1 DA I -69 " pdb=" NZ LYS L 73 " model vdw 0.876 3.120 nonbonded pdb=" OP1 DA I -69 " pdb=" CE LYS L 73 " model vdw 0.936 3.440 nonbonded pdb=" OP1 DG I -68 " pdb=" CD PRO L 19 " model vdw 1.751 3.440 nonbonded pdb=" O3' DA I -69 " pdb=" NH2 ARG L 74 " model vdw 1.840 3.120 nonbonded pdb=" P DA I -69 " pdb=" CE LYS L 73 " model vdw 1.967 3.800 ... (remaining 118155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.150 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.009 0.074 14550 Z= 0.703 Angle : 0.847 7.960 20935 Z= 0.691 Chirality : 0.054 0.207 2347 Planarity : 0.007 0.069 1614 Dihedral : 25.785 171.435 6230 Min Nonbonded Distance : 0.876 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.28 % Allowed : 8.75 % Favored : 88.97 % 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: -5.72 (0.17), residues: 913 helix: -4.46 (0.09), residues: 538 sheet: -4.09 (0.69), residues: 34 loop : -2.16 (0.26), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.012 0.002 TYR B 72 PHE 0.013 0.002 PHE K 45 TRP 0.005 0.002 TRP L 82 HIS 0.004 0.001 HIS L 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.70 (14550) covalent geometry : angle 0.84696 / 0.69 (20935) hydrogen bonds : bond 0.31427 / 20.67 ( 667) hydrogen bonds : angle 10.67049 / 7.37 ( 1658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8817 (mttt) cc_final: 0.8467 (mttp) REVERT: B 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8159 (m-10) REVERT: C 34 LEU cc_start: 0.8953 (mt) cc_final: 0.8728 (mm) REVERT: C 110 ASN cc_start: 0.8654 (t0) cc_final: 0.8436 (t0) REVERT: C 115 LEU cc_start: 0.8384 (mt) cc_final: 0.7994 (mp) REVERT: D 59 MET cc_start: 0.8367 (mmm) cc_final: 0.8049 (mmm) REVERT: D 91 ILE cc_start: 0.8561 (mm) cc_final: 0.8305 (mt) REVERT: D 103 LEU cc_start: 0.8636 (mt) cc_final: 0.8277 (mt) REVERT: F 73 THR cc_start: 0.7936 (m) cc_final: 0.7699 (m) REVERT: H 87 THR cc_start: 0.8808 (p) cc_final: 0.8441 (t) REVERT: A 90 MET cc_start: 0.8080 (mmm) cc_final: 0.7871 (mmt) REVERT: A 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7414 (mtt) REVERT: A 126 LEU cc_start: 0.9415 (tp) cc_final: 0.9167 (tp) REVERT: E 41 TYR cc_start: 0.8515 (m-80) cc_final: 0.8139 (m-10) REVERT: E 60 LEU cc_start: 0.8938 (mt) cc_final: 0.8710 (mt) REVERT: E 119 ILE cc_start: 0.9261 (pt) cc_final: 0.9010 (pt) REVERT: E 125 GLN cc_start: 0.8627 (mt0) cc_final: 0.8360 (mt0) outliers start: 18 outliers final: 7 residues processed: 323 average time/residue: 0.1429 time to fit residues: 59.8286 Evaluate side-chains 240 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 75 HIS C 68 ASN C 73 ASN D 44 GLN D 92 GLN F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 92 GLN K 64 ASN K 86 ASN A 108 ASN A 113 HIS L 64 ASN L 86 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.169828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106827 restraints weight = 20842.871| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.53 r_work: 0.3048 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14550 Z= 0.173 Angle : 0.761 9.494 20935 Z= 0.431 Chirality : 0.050 0.268 2347 Planarity : 0.006 0.060 1614 Dihedral : 29.559 167.437 4342 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.53 % Allowed : 17.24 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.23), residues: 913 helix: -1.67 (0.18), residues: 543 sheet: -3.86 (0.75), residues: 34 loop : -1.56 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.024 0.003 TYR D 80 PHE 0.015 0.002 PHE K 44 TRP 0.006 0.001 TRP K 21 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (14550) covalent geometry : angle 0.76133 / 0.43 (20935) hydrogen bonds : bond 0.08385 / 5.39 ( 667) hydrogen bonds : angle 3.68738 / 2.51 ( 1658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.9176 (tttt) cc_final: 0.8808 (tttt) REVERT: B 77 LYS cc_start: 0.8979 (mttt) cc_final: 0.8572 (mttp) REVERT: B 82 THR cc_start: 0.9024 (p) cc_final: 0.8711 (t) REVERT: B 98 TYR cc_start: 0.9044 (m-10) cc_final: 0.8466 (m-10) REVERT: C 34 LEU cc_start: 0.8967 (mt) cc_final: 0.8552 (mm) REVERT: C 73 ASN cc_start: 0.7650 (t0) cc_final: 0.6728 (t0) REVERT: C 115 LEU cc_start: 0.8346 (mt) cc_final: 0.7867 (mp) REVERT: D 59 MET cc_start: 0.8842 (mmm) cc_final: 0.8533 (mmm) REVERT: D 68 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8416 (tm-30) REVERT: F 73 THR cc_start: 0.8582 (m) cc_final: 0.8247 (m) REVERT: G 92 GLU cc_start: 0.8466 (pm20) cc_final: 0.8147 (pm20) REVERT: G 110 ASN cc_start: 0.8422 (t0) cc_final: 0.8078 (t0) REVERT: G 115 LEU cc_start: 0.8837 (mt) cc_final: 0.8614 (mt) REVERT: H 68 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8428 (mm-30) REVERT: H 117 LYS cc_start: 0.8556 (tppp) cc_final: 0.7645 (ttpp) REVERT: A 90 MET cc_start: 0.8598 (mmm) cc_final: 0.8348 (mmt) REVERT: A 116 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7037 (mtm-85) REVERT: A 130 ILE cc_start: 0.8929 (mm) cc_final: 0.8722 (mm) REVERT: E 39 HIS cc_start: 0.8598 (t70) cc_final: 0.8114 (t70) REVERT: E 41 TYR cc_start: 0.8386 (m-80) cc_final: 0.8130 (m-10) REVERT: E 119 ILE cc_start: 0.9380 (pt) cc_final: 0.9058 (pt) outliers start: 20 outliers final: 15 residues processed: 265 average time/residue: 0.1160 time to fit residues: 42.4354 Evaluate side-chains 254 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 118 optimal weight: 40.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 75 HIS H 46 HIS E 93 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.163440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099539 restraints weight = 20842.443| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.52 r_work: 0.2939 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14550 Z= 0.188 Angle : 0.691 7.955 20935 Z= 0.391 Chirality : 0.048 0.275 2347 Planarity : 0.005 0.053 1614 Dihedral : 30.124 160.859 4333 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.04 % Allowed : 20.28 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.26), residues: 913 helix: -0.07 (0.22), residues: 547 sheet: -4.02 (0.98), residues: 20 loop : -1.32 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.049 0.002 TYR H 80 PHE 0.013 0.001 PHE E 67 TRP 0.005 0.001 TRP K 82 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (14550) covalent geometry : angle 0.69122 / 0.39 (20935) hydrogen bonds : bond 0.07303 / 4.65 ( 667) hydrogen bonds : angle 3.20288 / 2.18 ( 1658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9393 (mttt) cc_final: 0.9036 (mttp) REVERT: B 79 LYS cc_start: 0.8397 (mptt) cc_final: 0.8169 (mmtm) REVERT: B 82 THR cc_start: 0.9100 (p) cc_final: 0.8870 (t) REVERT: B 84 MET cc_start: 0.8140 (mmt) cc_final: 0.7931 (mmt) REVERT: B 98 TYR cc_start: 0.9140 (m-10) cc_final: 0.8588 (m-10) REVERT: C 34 LEU cc_start: 0.9000 (mt) cc_final: 0.8461 (mt) REVERT: C 73 ASN cc_start: 0.7608 (t0) cc_final: 0.6788 (t0) REVERT: C 115 LEU cc_start: 0.8656 (mt) cc_final: 0.8388 (mp) REVERT: D 59 MET cc_start: 0.8988 (mmm) cc_final: 0.8723 (tpp) REVERT: D 80 TYR cc_start: 0.8934 (m-10) cc_final: 0.8329 (m-10) REVERT: D 91 ILE cc_start: 0.8987 (mm) cc_final: 0.8621 (mt) REVERT: D 105 LYS cc_start: 0.9046 (tppp) cc_final: 0.8695 (mppt) REVERT: F 73 THR cc_start: 0.8868 (m) cc_final: 0.8530 (m) REVERT: F 74 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: F 78 ARG cc_start: 0.9168 (mtt90) cc_final: 0.8739 (mtp180) REVERT: G 73 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (t0) REVERT: G 75 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7964 (mppt) REVERT: G 92 GLU cc_start: 0.8364 (pm20) cc_final: 0.8069 (pm20) REVERT: G 110 ASN cc_start: 0.8809 (t0) cc_final: 0.8487 (t0) REVERT: H 31 LYS cc_start: 0.8624 (mppt) cc_final: 0.8402 (mppt) REVERT: H 87 THR cc_start: 0.8758 (p) cc_final: 0.8507 (t) REVERT: H 109 SER cc_start: 0.8997 (t) cc_final: 0.8751 (p) REVERT: H 110 GLU cc_start: 0.9172 (tp30) cc_final: 0.8787 (tp30) REVERT: H 117 LYS cc_start: 0.8592 (tppp) cc_final: 0.7862 (ttpp) REVERT: K 15 MET cc_start: 0.6634 (mtt) cc_final: 0.6182 (mtt) REVERT: K 16 LYS cc_start: 0.8081 (tptp) cc_final: 0.7832 (tptt) REVERT: A 90 MET cc_start: 0.8638 (mmm) cc_final: 0.8288 (mmt) REVERT: A 120 MET cc_start: 0.8057 (mtp) cc_final: 0.7818 (mtm) REVERT: E 39 HIS cc_start: 0.8679 (t70) cc_final: 0.8151 (t70) REVERT: E 105 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8791 (mm-30) REVERT: E 119 ILE cc_start: 0.9413 (pt) cc_final: 0.9166 (pt) REVERT: L 79 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5552 (pt0) outliers start: 24 outliers final: 17 residues processed: 269 average time/residue: 0.1199 time to fit residues: 44.3082 Evaluate side-chains 263 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN F 93 GLN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097194 restraints weight = 20635.636| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.42 r_work: 0.2872 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14550 Z= 0.202 Angle : 0.686 10.400 20935 Z= 0.384 Chirality : 0.047 0.270 2347 Planarity : 0.005 0.048 1614 Dihedral : 30.055 157.116 4329 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.56 % Allowed : 22.05 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 913 helix: 0.68 (0.23), residues: 548 sheet: -4.39 (0.96), residues: 20 loop : -1.31 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.027 0.002 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.005 0.001 TRP K 21 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (14550) covalent geometry : angle 0.68624 / 0.38 (20935) hydrogen bonds : bond 0.06914 / 4.44 ( 667) hydrogen bonds : angle 3.12712 / 2.13 ( 1658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9527 (mttt) cc_final: 0.9164 (mttp) REVERT: B 82 THR cc_start: 0.9202 (p) cc_final: 0.8951 (t) REVERT: B 84 MET cc_start: 0.8544 (mmt) cc_final: 0.8302 (tpp) REVERT: B 88 TYR cc_start: 0.9105 (m-10) cc_final: 0.8479 (m-10) REVERT: B 98 TYR cc_start: 0.9260 (m-10) cc_final: 0.8711 (m-10) REVERT: C 73 ASN cc_start: 0.7608 (t0) cc_final: 0.6829 (t0) REVERT: C 94 ASN cc_start: 0.8509 (t0) cc_final: 0.8011 (t0) REVERT: C 112 GLN cc_start: 0.8114 (mm110) cc_final: 0.7897 (tp40) REVERT: D 80 TYR cc_start: 0.8972 (m-10) cc_final: 0.8375 (m-10) REVERT: D 102 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7282 (mm-30) REVERT: D 105 LYS cc_start: 0.9035 (tppp) cc_final: 0.8731 (mtmm) REVERT: D 110 GLU cc_start: 0.9287 (tp30) cc_final: 0.9078 (tp30) REVERT: D 117 LYS cc_start: 0.9067 (tppp) cc_final: 0.8837 (ttmm) REVERT: D 122 LYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6343 (ttpp) REVERT: F 73 THR cc_start: 0.9073 (m) cc_final: 0.8754 (m) REVERT: F 74 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: F 78 ARG cc_start: 0.9175 (mtt90) cc_final: 0.8738 (mtm-85) REVERT: G 33 LEU cc_start: 0.8962 (mt) cc_final: 0.8704 (mt) REVERT: G 74 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8547 (mmmm) REVERT: G 92 GLU cc_start: 0.8504 (pm20) cc_final: 0.8087 (pm20) REVERT: H 31 LYS cc_start: 0.8754 (mppt) cc_final: 0.8519 (mppt) REVERT: H 65 ASP cc_start: 0.9031 (t0) cc_final: 0.8771 (t0) REVERT: H 68 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8629 (mm-30) REVERT: H 84 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8374 (p) REVERT: H 117 LYS cc_start: 0.8636 (tppp) cc_final: 0.8022 (ttpp) REVERT: K 14 LYS cc_start: 0.6345 (tppt) cc_final: 0.5014 (mtmt) REVERT: K 16 LYS cc_start: 0.8050 (tptp) cc_final: 0.7121 (tppt) REVERT: A 42 ARG cc_start: 0.7264 (mmm-85) cc_final: 0.6787 (mmm-85) REVERT: A 90 MET cc_start: 0.8595 (mmm) cc_final: 0.8348 (mmp) REVERT: A 108 ASN cc_start: 0.9237 (t0) cc_final: 0.8652 (t0) REVERT: A 120 MET cc_start: 0.8218 (mtp) cc_final: 0.7973 (mtm) REVERT: E 94 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 105 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8871 (mm-30) REVERT: E 119 ILE cc_start: 0.9401 (pt) cc_final: 0.9045 (pt) outliers start: 36 outliers final: 23 residues processed: 272 average time/residue: 0.1257 time to fit residues: 46.2680 Evaluate side-chains 266 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN G 73 ASN E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095867 restraints weight = 20755.585| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.45 r_work: 0.2891 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14550 Z= 0.151 Angle : 0.625 9.172 20935 Z= 0.358 Chirality : 0.044 0.260 2347 Planarity : 0.004 0.047 1614 Dihedral : 29.933 156.884 4329 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.06 % Allowed : 24.08 % Favored : 71.86 % 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: 0.21 (0.28), residues: 913 helix: 1.10 (0.23), residues: 550 sheet: -4.29 (0.95), residues: 20 loop : -1.12 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.019 0.002 TYR H 80 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 82 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (14550) covalent geometry : angle 0.62543 / 0.36 (20935) hydrogen bonds : bond 0.06209 / 3.95 ( 667) hydrogen bonds : angle 2.94842 / 2.02 ( 1658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.233 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: B 27 GLN cc_start: 0.8464 (tp-100) cc_final: 0.8246 (mm110) REVERT: B 77 LYS cc_start: 0.9574 (mttt) cc_final: 0.9209 (mttp) REVERT: B 82 THR cc_start: 0.9158 (p) cc_final: 0.8940 (t) REVERT: B 88 TYR cc_start: 0.9163 (m-10) cc_final: 0.8900 (m-80) REVERT: B 98 TYR cc_start: 0.9264 (m-10) cc_final: 0.8646 (m-10) REVERT: C 73 ASN cc_start: 0.7711 (t0) cc_final: 0.6984 (t0) REVERT: C 94 ASN cc_start: 0.8591 (t0) cc_final: 0.8066 (t0) REVERT: C 100 VAL cc_start: 0.9588 (OUTLIER) cc_final: 0.9361 (p) REVERT: D 102 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 105 LYS cc_start: 0.9029 (tppp) cc_final: 0.8732 (mtmm) REVERT: D 117 LYS cc_start: 0.9119 (tppp) cc_final: 0.8882 (ttmm) REVERT: D 122 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6408 (ttpp) REVERT: F 73 THR cc_start: 0.9163 (m) cc_final: 0.8878 (m) REVERT: F 74 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: F 78 ARG cc_start: 0.9189 (mtt90) cc_final: 0.8977 (mtm-85) REVERT: F 84 MET cc_start: 0.8050 (mmm) cc_final: 0.7781 (mmm) REVERT: F 88 TYR cc_start: 0.9271 (m-10) cc_final: 0.8903 (m-10) REVERT: G 33 LEU cc_start: 0.8996 (mt) cc_final: 0.8754 (mt) REVERT: G 92 GLU cc_start: 0.8643 (pm20) cc_final: 0.8425 (pm20) REVERT: H 65 ASP cc_start: 0.9073 (t0) cc_final: 0.8789 (t0) REVERT: H 68 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8638 (mm-30) REVERT: H 117 LYS cc_start: 0.8717 (tppp) cc_final: 0.8063 (ttpp) REVERT: A 42 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6922 (mmm-85) REVERT: A 90 MET cc_start: 0.8589 (mmm) cc_final: 0.8296 (mmt) REVERT: A 108 ASN cc_start: 0.9194 (t0) cc_final: 0.8632 (t0) REVERT: A 120 MET cc_start: 0.8248 (mtp) cc_final: 0.8043 (mtp) REVERT: E 73 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8449 (tt0) REVERT: E 76 GLN cc_start: 0.9182 (tp40) cc_final: 0.8957 (mm-40) REVERT: E 105 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8865 (mm-30) outliers start: 32 outliers final: 22 residues processed: 265 average time/residue: 0.1215 time to fit residues: 44.1101 Evaluate side-chains 270 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN G 73 ASN A 39 HIS E 39 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096416 restraints weight = 20575.622| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.43 r_work: 0.2897 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14550 Z= 0.137 Angle : 0.610 8.084 20935 Z= 0.351 Chirality : 0.043 0.262 2347 Planarity : 0.004 0.046 1614 Dihedral : 29.854 156.426 4329 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.56 % Allowed : 24.97 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 913 helix: 1.28 (0.23), residues: 558 sheet: -4.22 (0.94), residues: 20 loop : -1.01 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.035 0.001 TYR H 80 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (14550) covalent geometry : angle 0.60954 / 0.35 (20935) hydrogen bonds : bond 0.05960 / 3.80 ( 667) hydrogen bonds : angle 2.84614 / 1.96 ( 1658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 0.308 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: B 27 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8197 (mm110) REVERT: B 74 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8793 (mm-30) REVERT: B 77 LYS cc_start: 0.9562 (mttt) cc_final: 0.9191 (mttp) REVERT: B 84 MET cc_start: 0.8564 (mmt) cc_final: 0.7866 (mmt) REVERT: B 88 TYR cc_start: 0.9156 (m-10) cc_final: 0.8850 (m-80) REVERT: B 98 TYR cc_start: 0.9252 (m-10) cc_final: 0.8572 (m-10) REVERT: C 73 ASN cc_start: 0.7872 (t0) cc_final: 0.7153 (t0) REVERT: C 94 ASN cc_start: 0.8521 (t0) cc_final: 0.7955 (t0) REVERT: C 100 VAL cc_start: 0.9607 (OUTLIER) cc_final: 0.9337 (p) REVERT: C 104 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8756 (mt0) REVERT: D 102 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 105 LYS cc_start: 0.9003 (tppp) cc_final: 0.8762 (mtmm) REVERT: F 73 THR cc_start: 0.9145 (m) cc_final: 0.8832 (m) REVERT: F 74 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: F 78 ARG cc_start: 0.9190 (mtt90) cc_final: 0.8913 (mtm-85) REVERT: G 33 LEU cc_start: 0.8922 (mt) cc_final: 0.8674 (mt) REVERT: G 73 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8134 (t0) REVERT: G 92 GLU cc_start: 0.8662 (pm20) cc_final: 0.8394 (pm20) REVERT: H 65 ASP cc_start: 0.9072 (t0) cc_final: 0.8776 (t0) REVERT: H 68 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8592 (mm-30) REVERT: H 117 LYS cc_start: 0.8686 (tppp) cc_final: 0.8055 (ttpp) REVERT: K 14 LYS cc_start: 0.6251 (tppt) cc_final: 0.4296 (mptt) REVERT: A 42 ARG cc_start: 0.7228 (mmm-85) cc_final: 0.6938 (mmm-85) REVERT: A 85 GLN cc_start: 0.8720 (mt0) cc_final: 0.8498 (mt0) REVERT: A 90 MET cc_start: 0.8555 (mmm) cc_final: 0.8187 (mmp) REVERT: A 120 MET cc_start: 0.8208 (mtp) cc_final: 0.7996 (mtp) REVERT: E 41 TYR cc_start: 0.8737 (m-10) cc_final: 0.8442 (m-10) REVERT: E 73 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8431 (tt0) REVERT: E 76 GLN cc_start: 0.9189 (tp40) cc_final: 0.8971 (mm-40) REVERT: E 105 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8855 (mm-30) outliers start: 36 outliers final: 26 residues processed: 262 average time/residue: 0.1225 time to fit residues: 43.7407 Evaluate side-chains 270 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 110 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN G 73 ASN A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN L 78 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095450 restraints weight = 20684.536| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.50 r_work: 0.2882 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14550 Z= 0.152 Angle : 0.626 10.667 20935 Z= 0.357 Chirality : 0.044 0.259 2347 Planarity : 0.004 0.046 1614 Dihedral : 29.841 155.934 4323 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 25.35 % Favored : 69.58 % 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: 0.60 (0.28), residues: 913 helix: 1.43 (0.23), residues: 555 sheet: -4.20 (0.92), residues: 20 loop : -1.05 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.039 0.002 TYR H 80 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 21 HIS 0.016 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (14550) covalent geometry : angle 0.62571 / 0.36 (20935) hydrogen bonds : bond 0.05986 / 3.83 ( 667) hydrogen bonds : angle 2.90519 / 2.00 ( 1658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 0.270 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: B 27 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8221 (mm110) REVERT: B 74 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8758 (mm-30) REVERT: B 77 LYS cc_start: 0.9584 (mttt) cc_final: 0.9256 (mttp) REVERT: B 84 MET cc_start: 0.8591 (mmt) cc_final: 0.7756 (tpp) REVERT: B 88 TYR cc_start: 0.9167 (m-10) cc_final: 0.8626 (m-80) REVERT: B 98 TYR cc_start: 0.9238 (m-10) cc_final: 0.8560 (m-10) REVERT: C 73 ASN cc_start: 0.7948 (t0) cc_final: 0.7215 (t0) REVERT: C 94 ASN cc_start: 0.8549 (t0) cc_final: 0.7979 (t0) REVERT: C 100 VAL cc_start: 0.9585 (OUTLIER) cc_final: 0.9341 (p) REVERT: D 39 TYR cc_start: 0.8223 (t80) cc_final: 0.7761 (t80) REVERT: D 80 TYR cc_start: 0.8874 (m-10) cc_final: 0.8336 (m-10) REVERT: D 102 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7114 (mm-30) REVERT: D 105 LYS cc_start: 0.9015 (tppp) cc_final: 0.8726 (mtmm) REVERT: F 24 ASP cc_start: 0.8678 (t0) cc_final: 0.8160 (p0) REVERT: F 73 THR cc_start: 0.9150 (m) cc_final: 0.8826 (m) REVERT: F 74 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: F 78 ARG cc_start: 0.9213 (mtt90) cc_final: 0.8966 (mtm-85) REVERT: G 33 LEU cc_start: 0.8950 (mt) cc_final: 0.8697 (mt) REVERT: G 73 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8194 (t0) REVERT: G 90 ASP cc_start: 0.8967 (t70) cc_final: 0.8054 (t0) REVERT: G 92 GLU cc_start: 0.8677 (pm20) cc_final: 0.8311 (pm20) REVERT: H 65 ASP cc_start: 0.9091 (t0) cc_final: 0.8781 (t0) REVERT: H 68 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8624 (mm-30) REVERT: H 117 LYS cc_start: 0.8682 (tppp) cc_final: 0.8014 (ttpp) REVERT: A 79 LYS cc_start: 0.8926 (tttp) cc_final: 0.8500 (ttmt) REVERT: A 108 ASN cc_start: 0.9097 (t0) cc_final: 0.8598 (t0) REVERT: A 120 MET cc_start: 0.8219 (mtp) cc_final: 0.8006 (mtp) REVERT: E 73 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8444 (tt0) REVERT: E 76 GLN cc_start: 0.9194 (tp40) cc_final: 0.8909 (mm-40) REVERT: E 105 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8852 (mm-30) outliers start: 40 outliers final: 32 residues processed: 257 average time/residue: 0.1175 time to fit residues: 41.4988 Evaluate side-chains 277 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 115 optimal weight: 50.0000 chunk 114 optimal weight: 0.2980 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN A 108 ASN E 39 HIS E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096773 restraints weight = 20319.283| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.43 r_work: 0.2897 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14550 Z= 0.136 Angle : 0.609 11.306 20935 Z= 0.350 Chirality : 0.043 0.257 2347 Planarity : 0.004 0.045 1614 Dihedral : 29.771 155.763 4323 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.44 % Allowed : 26.62 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 913 helix: 1.63 (0.23), residues: 554 sheet: -4.14 (0.93), residues: 20 loop : -0.95 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.035 0.001 TYR H 80 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP K 82 HIS 0.013 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (14550) covalent geometry : angle 0.60903 / 0.35 (20935) hydrogen bonds : bond 0.05784 / 3.69 ( 667) hydrogen bonds : angle 2.84834 / 1.96 ( 1658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.276 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: B 74 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8673 (mm-30) REVERT: B 77 LYS cc_start: 0.9589 (mttt) cc_final: 0.9272 (mttp) REVERT: B 84 MET cc_start: 0.8611 (mmt) cc_final: 0.7831 (tpp) REVERT: B 88 TYR cc_start: 0.9179 (m-10) cc_final: 0.8653 (m-80) REVERT: B 98 TYR cc_start: 0.9236 (m-10) cc_final: 0.8571 (m-10) REVERT: C 73 ASN cc_start: 0.7940 (t0) cc_final: 0.7209 (t0) REVERT: C 94 ASN cc_start: 0.8573 (t0) cc_final: 0.7988 (t0) REVERT: C 100 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9263 (p) REVERT: D 80 TYR cc_start: 0.8865 (m-10) cc_final: 0.8312 (m-10) REVERT: D 102 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7296 (mm-30) REVERT: D 105 LYS cc_start: 0.9028 (tppp) cc_final: 0.8709 (mtmm) REVERT: F 73 THR cc_start: 0.9132 (m) cc_final: 0.8786 (m) REVERT: F 74 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: F 78 ARG cc_start: 0.9216 (mtt90) cc_final: 0.9009 (mtm-85) REVERT: G 33 LEU cc_start: 0.8971 (mt) cc_final: 0.8720 (mt) REVERT: G 90 ASP cc_start: 0.8993 (t70) cc_final: 0.8278 (t0) REVERT: G 92 GLU cc_start: 0.8682 (pm20) cc_final: 0.8345 (pm20) REVERT: H 65 ASP cc_start: 0.9087 (t0) cc_final: 0.8775 (t0) REVERT: H 68 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8626 (mm-30) REVERT: H 117 LYS cc_start: 0.8721 (tppp) cc_final: 0.8063 (ttpp) REVERT: K 14 LYS cc_start: 0.5696 (tppt) cc_final: 0.3393 (mmtt) REVERT: A 79 LYS cc_start: 0.8969 (tttp) cc_final: 0.8668 (ttmt) REVERT: A 85 GLN cc_start: 0.8813 (mt0) cc_final: 0.8492 (mt0) REVERT: A 108 ASN cc_start: 0.9188 (t0) cc_final: 0.8649 (t0) REVERT: A 120 MET cc_start: 0.8228 (mtp) cc_final: 0.8025 (mtp) REVERT: E 73 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8363 (tt0) REVERT: E 76 GLN cc_start: 0.9238 (tp40) cc_final: 0.8950 (mm-40) REVERT: E 105 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8809 (mm-30) REVERT: L 79 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5742 (pt0) outliers start: 35 outliers final: 29 residues processed: 259 average time/residue: 0.1215 time to fit residues: 42.9718 Evaluate side-chains 275 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 73 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.156385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092359 restraints weight = 20494.431| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.40 r_work: 0.2826 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14550 Z= 0.242 Angle : 0.694 9.863 20935 Z= 0.384 Chirality : 0.046 0.250 2347 Planarity : 0.005 0.045 1614 Dihedral : 29.902 154.698 4323 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.08 % Allowed : 24.97 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 913 helix: 1.52 (0.23), residues: 553 sheet: -4.07 (0.93), residues: 20 loop : -0.96 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 40 TYR 0.035 0.002 TYR H 80 PHE 0.012 0.001 PHE F 100 TRP 0.003 0.001 TRP K 82 HIS 0.027 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (14550) covalent geometry : angle 0.69411 / 0.38 (20935) hydrogen bonds : bond 0.06756 / 4.35 ( 667) hydrogen bonds : angle 3.14297 / 2.16 ( 1658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.246 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: B 27 GLN cc_start: 0.9028 (mm110) cc_final: 0.8739 (mm110) REVERT: B 74 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8628 (mm-30) REVERT: B 77 LYS cc_start: 0.9585 (mttt) cc_final: 0.9356 (mttm) REVERT: B 84 MET cc_start: 0.8689 (mmt) cc_final: 0.7962 (tpp) REVERT: B 88 TYR cc_start: 0.9224 (m-10) cc_final: 0.8925 (m-80) REVERT: B 98 TYR cc_start: 0.9274 (m-10) cc_final: 0.8564 (m-10) REVERT: C 73 ASN cc_start: 0.8330 (t0) cc_final: 0.7493 (t0) REVERT: D 102 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 105 LYS cc_start: 0.9102 (tppp) cc_final: 0.8798 (mtmm) REVERT: F 73 THR cc_start: 0.9183 (m) cc_final: 0.8850 (m) REVERT: F 74 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: F 78 ARG cc_start: 0.9289 (mtt90) cc_final: 0.9009 (mtm-85) REVERT: F 88 TYR cc_start: 0.9091 (m-10) cc_final: 0.8487 (m-80) REVERT: G 33 LEU cc_start: 0.9105 (mt) cc_final: 0.8869 (mt) REVERT: G 90 ASP cc_start: 0.8533 (t70) cc_final: 0.7628 (t0) REVERT: G 92 GLU cc_start: 0.8715 (pm20) cc_final: 0.8379 (pm20) REVERT: H 31 LYS cc_start: 0.8723 (mppt) cc_final: 0.8503 (mppt) REVERT: H 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8798 (t0) REVERT: H 68 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8671 (mm-30) REVERT: H 102 GLU cc_start: 0.7927 (tp30) cc_final: 0.6813 (tm-30) REVERT: H 110 GLU cc_start: 0.9234 (tp30) cc_final: 0.8784 (tp30) REVERT: K 14 LYS cc_start: 0.5814 (tppt) cc_final: 0.3459 (mmtt) REVERT: A 79 LYS cc_start: 0.9022 (tttp) cc_final: 0.8668 (ttmt) REVERT: A 85 GLN cc_start: 0.8901 (mt0) cc_final: 0.8562 (mt0) REVERT: A 90 MET cc_start: 0.8500 (mmp) cc_final: 0.8265 (mmt) REVERT: A 108 ASN cc_start: 0.9186 (t0) cc_final: 0.8665 (t0) REVERT: A 120 MET cc_start: 0.8393 (mtp) cc_final: 0.7843 (mtp) REVERT: A 123 ASP cc_start: 0.9142 (m-30) cc_final: 0.8838 (m-30) REVERT: E 41 TYR cc_start: 0.9042 (m-10) cc_final: 0.8565 (m-10) REVERT: E 45 THR cc_start: 0.8932 (t) cc_final: 0.8612 (p) REVERT: E 73 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8408 (tt0) REVERT: E 76 GLN cc_start: 0.9338 (tp40) cc_final: 0.9058 (mm-40) REVERT: E 105 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8837 (mm-30) REVERT: L 79 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5751 (pt0) outliers start: 48 outliers final: 38 residues processed: 279 average time/residue: 0.1146 time to fit residues: 43.6987 Evaluate side-chains 292 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.156472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092311 restraints weight = 20554.806| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.41 r_work: 0.2829 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 14550 Z= 0.230 Angle : 0.873 59.194 20935 Z= 0.510 Chirality : 0.045 0.250 2347 Planarity : 0.005 0.073 1614 Dihedral : 29.908 154.767 4323 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.45 % Allowed : 25.86 % Favored : 68.69 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.28), residues: 913 helix: 1.53 (0.22), residues: 553 sheet: -4.07 (0.93), residues: 20 loop : -0.97 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.045 0.002 TYR H 37 PHE 0.011 0.001 PHE F 100 TRP 0.003 0.001 TRP K 82 HIS 0.015 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (14550) covalent geometry : angle 0.87263 / 0.51 (20935) hydrogen bonds : bond 0.06688 / 4.30 ( 667) hydrogen bonds : angle 3.12400 / 2.15 ( 1658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.262 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: B 27 GLN cc_start: 0.9025 (mm110) cc_final: 0.8734 (mm110) REVERT: B 77 LYS cc_start: 0.9586 (mttt) cc_final: 0.9359 (mttm) REVERT: B 84 MET cc_start: 0.8690 (mmt) cc_final: 0.7964 (tpp) REVERT: B 88 TYR cc_start: 0.9221 (m-10) cc_final: 0.8923 (m-80) REVERT: B 98 TYR cc_start: 0.9266 (m-10) cc_final: 0.8556 (m-10) REVERT: C 73 ASN cc_start: 0.8294 (t0) cc_final: 0.7462 (t0) REVERT: C 100 VAL cc_start: 0.9505 (t) cc_final: 0.9120 (p) REVERT: D 102 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 105 LYS cc_start: 0.9106 (tppp) cc_final: 0.8798 (mtmm) REVERT: F 73 THR cc_start: 0.9156 (m) cc_final: 0.8851 (m) REVERT: F 74 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: F 78 ARG cc_start: 0.9271 (mtt90) cc_final: 0.9049 (mtm-85) REVERT: F 88 TYR cc_start: 0.9095 (m-10) cc_final: 0.8482 (m-80) REVERT: G 33 LEU cc_start: 0.9101 (mt) cc_final: 0.8863 (mt) REVERT: G 73 ASN cc_start: 0.8196 (t0) cc_final: 0.7485 (t0) REVERT: G 90 ASP cc_start: 0.8540 (t70) cc_final: 0.7377 (t70) REVERT: G 92 GLU cc_start: 0.8756 (pm20) cc_final: 0.8314 (pm20) REVERT: H 31 LYS cc_start: 0.8714 (mppt) cc_final: 0.8496 (mppt) REVERT: H 65 ASP cc_start: 0.9120 (t0) cc_final: 0.8796 (t0) REVERT: H 68 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8664 (mm-30) REVERT: H 102 GLU cc_start: 0.7920 (tp30) cc_final: 0.6788 (tm-30) REVERT: H 110 GLU cc_start: 0.9232 (tp30) cc_final: 0.8799 (tp30) REVERT: K 14 LYS cc_start: 0.5828 (tppt) cc_final: 0.3464 (mmtt) REVERT: A 85 GLN cc_start: 0.8911 (mt0) cc_final: 0.8571 (mt0) REVERT: A 108 ASN cc_start: 0.9165 (t0) cc_final: 0.8661 (t0) REVERT: A 120 MET cc_start: 0.8398 (mtp) cc_final: 0.7844 (mtp) REVERT: A 123 ASP cc_start: 0.9143 (m-30) cc_final: 0.8840 (m-30) REVERT: E 41 TYR cc_start: 0.9039 (m-10) cc_final: 0.8675 (m-10) REVERT: E 45 THR cc_start: 0.8931 (t) cc_final: 0.8609 (p) REVERT: E 73 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8398 (tt0) REVERT: E 76 GLN cc_start: 0.9330 (tp40) cc_final: 0.9046 (mm-40) REVERT: E 105 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8829 (mm-30) REVERT: L 79 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5767 (pt0) outliers start: 43 outliers final: 38 residues processed: 272 average time/residue: 0.1206 time to fit residues: 45.0971 Evaluate side-chains 291 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.156434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091878 restraints weight = 20698.233| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.43 r_work: 0.2827 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 14550 Z= 0.230 Angle : 0.873 59.194 20935 Z= 0.510 Chirality : 0.045 0.250 2347 Planarity : 0.005 0.073 1614 Dihedral : 29.908 154.767 4323 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.20 % Allowed : 26.49 % Favored : 68.31 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.28), residues: 913 helix: 1.53 (0.22), residues: 553 sheet: -4.07 (0.93), residues: 20 loop : -0.97 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.045 0.002 TYR H 37 PHE 0.011 0.001 PHE F 100 TRP 0.003 0.001 TRP K 82 HIS 0.015 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (14550) covalent geometry : angle 0.87263 / 0.51 (20935) hydrogen bonds : bond 0.06688 / 4.30 ( 667) hydrogen bonds : angle 3.12400 / 2.15 ( 1658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.45 seconds wall clock time: 50 minutes 10.13 seconds (3010.13 seconds total)