Starting phenix.real_space_refine on Fri Jul 3 09:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbn_16546/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbn_16546/07_2026/8cbn_16546.map" } 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-dev-6108/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: 2.48, 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: 0.90 Conformation dependent library (CDL) restraints added in 392.3 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: 1.71 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: 2.13 Time building geometry restraints manager: 1.25 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: 19341 1.59 - 3.18: 1516 3.18 - 4.78: 56 4.78 - 6.37: 15 6.37 - 7.96: 7 Bond angle restraints: 20935 Sorted by residual: 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 angle pdb=" N3 DT J 13 " pdb=" C4 DT J 13 " pdb=" O4 DT J 13 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 34 " pdb=" C4 DT I 34 " pdb=" O4 DT I 34 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.300 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- 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= 0.702 Angle : 0.842 7.960 20935 Z= 0.686 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 0.84202 / 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 : 0.226 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: 0.8726 (mm) REVERT: C 110 ASN cc_start: 0.8654 (t0) cc_final: 0.8437 (t0) REVERT: C 115 LEU cc_start: 0.8384 (mt) cc_final: 0.7998 (mp) REVERT: D 59 MET cc_start: 0.8367 (mmm) cc_final: 0.8047 (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 43 VAL cc_start: 0.9461 (t) cc_final: 0.9260 (t) 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: 0.7870 (mmt) REVERT: A 120 MET cc_start: 0.7883 (mtp) cc_final: 0.7413 (mtt) REVERT: A 126 LEU cc_start: 0.9415 (tp) cc_final: 0.9168 (tp) REVERT: E 41 TYR cc_start: 0.8515 (m-80) cc_final: 0.8265 (m-10) REVERT: E 60 LEU cc_start: 0.8938 (mt) cc_final: 0.8699 (mt) REVERT: E 119 ILE cc_start: 0.9261 (pt) cc_final: 0.9011 (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: 0.1609 time to fit residues: 67.2239 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 : 0.420 ------------------------------------------------------------------------------- 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: 8.9990 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106974 restraints weight = 20879.734| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.54 r_work: 0.3048 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14550 Z= 0.177 Angle : 0.766 9.179 20935 Z= 0.432 Chirality : 0.051 0.261 2347 Planarity : 0.006 0.059 1614 Dihedral : 29.686 168.667 4342 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.41 % Allowed : 17.36 % 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: -2.79 (0.23), residues: 913 helix: -1.71 (0.18), residues: 543 sheet: -3.87 (0.75), residues: 34 loop : -1.55 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.023 0.003 TYR D 80 PHE 0.012 0.002 PHE K 44 TRP 0.006 0.001 TRP K 21 HIS 0.010 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (14550) covalent geometry : angle 0.76583 / 0.43 (20935) hydrogen bonds : bond 0.08501 / 5.48 ( 667) hydrogen bonds : angle 3.67821 / 2.50 ( 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 268 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.9184 (tttt) cc_final: 0.8820 (tttt) REVERT: B 77 LYS cc_start: 0.8985 (mttt) cc_final: 0.8578 (mttp) REVERT: B 82 THR cc_start: 0.9035 (p) cc_final: 0.8719 (t) REVERT: B 98 TYR cc_start: 0.9054 (m-10) cc_final: 0.8468 (m-10) REVERT: C 34 LEU cc_start: 0.8967 (mt) cc_final: 0.8538 (mt) REVERT: C 73 ASN cc_start: 0.7617 (t0) cc_final: 0.6748 (t0) REVERT: C 115 LEU cc_start: 0.8345 (mt) cc_final: 0.7866 (mp) REVERT: D 59 MET cc_start: 0.8915 (mmm) cc_final: 0.8604 (mmm) REVERT: D 68 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: D 91 ILE cc_start: 0.8801 (mm) cc_final: 0.8504 (mt) REVERT: F 73 THR cc_start: 0.8575 (m) cc_final: 0.8242 (m) REVERT: F 84 MET cc_start: 0.8597 (mmm) cc_final: 0.8176 (mmt) REVERT: G 92 GLU cc_start: 0.8486 (pm20) cc_final: 0.8166 (pm20) REVERT: G 110 ASN cc_start: 0.8422 (t0) cc_final: 0.8082 (t0) REVERT: G 115 LEU cc_start: 0.8835 (mt) cc_final: 0.8618 (mt) REVERT: H 68 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8430 (mm-30) REVERT: H 117 LYS cc_start: 0.8560 (tppp) cc_final: 0.7640 (ttpp) REVERT: A 41 TYR cc_start: 0.7864 (m-80) cc_final: 0.7592 (m-80) REVERT: A 90 MET cc_start: 0.8602 (mmm) cc_final: 0.8352 (mmt) REVERT: A 116 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: A 120 MET cc_start: 0.7654 (mtp) cc_final: 0.7309 (mtp) REVERT: E 39 HIS cc_start: 0.8640 (t70) cc_final: 0.8158 (t70) REVERT: E 105 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8910 (mm-30) REVERT: E 119 ILE cc_start: 0.9404 (pt) cc_final: 0.9092 (pt) outliers start: 19 outliers final: 14 residues processed: 263 average time/residue: 0.1148 time to fit residues: 41.3591 Evaluate side-chains 252 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 E residue 105 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: 9.9990 chunk 73 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 118 optimal weight: 30.0000 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 46 HIS D 92 GLN F 75 HIS H 46 HIS A 39 HIS E 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100390 restraints weight = 20882.234| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.47 r_work: 0.2949 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14550 Z= 0.179 Angle : 0.673 8.041 20935 Z= 0.385 Chirality : 0.047 0.248 2347 Planarity : 0.005 0.052 1614 Dihedral : 30.154 162.272 4333 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.66 % Allowed : 20.41 % Favored : 76.93 % 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: -0.87 (0.27), residues: 913 helix: 0.07 (0.22), residues: 549 sheet: -4.07 (0.99), residues: 20 loop : -1.29 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.040 0.003 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 82 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (14550) covalent geometry : angle 0.67300 / 0.39 (20935) hydrogen bonds : bond 0.07297 / 4.63 ( 667) hydrogen bonds : angle 3.25908 / 2.22 ( 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 271 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9378 (mttt) cc_final: 0.8976 (mttp) REVERT: B 79 LYS cc_start: 0.8415 (mptt) cc_final: 0.8186 (mmtm) REVERT: B 82 THR cc_start: 0.9088 (p) cc_final: 0.8811 (t) REVERT: B 84 MET cc_start: 0.8385 (mmt) cc_final: 0.7863 (mmt) REVERT: B 88 TYR cc_start: 0.9047 (m-80) cc_final: 0.8433 (m-80) REVERT: B 98 TYR cc_start: 0.9153 (m-10) cc_final: 0.8510 (m-10) REVERT: C 13 LYS cc_start: 0.7591 (tppt) cc_final: 0.7382 (tppt) REVERT: C 34 LEU cc_start: 0.9032 (mt) cc_final: 0.8507 (mt) REVERT: C 73 ASN cc_start: 0.7635 (t0) cc_final: 0.6790 (t0) REVERT: C 115 LEU cc_start: 0.8762 (mt) cc_final: 0.8474 (mp) REVERT: D 59 MET cc_start: 0.8963 (mmm) cc_final: 0.8701 (tpp) REVERT: D 80 TYR cc_start: 0.8860 (m-10) cc_final: 0.8564 (m-80) REVERT: D 98 LEU cc_start: 0.9113 (mt) cc_final: 0.8912 (mt) REVERT: F 73 THR cc_start: 0.8861 (m) cc_final: 0.8542 (m) REVERT: F 74 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: G 75 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7967 (mppt) REVERT: G 91 GLU cc_start: 0.8245 (pm20) cc_final: 0.7941 (pm20) REVERT: G 92 GLU cc_start: 0.8373 (pm20) cc_final: 0.7654 (pm20) REVERT: G 110 ASN cc_start: 0.8780 (t0) cc_final: 0.8492 (t0) REVERT: H 31 LYS cc_start: 0.8650 (mppt) cc_final: 0.8415 (mppt) REVERT: H 87 THR cc_start: 0.8764 (p) cc_final: 0.8517 (t) REVERT: H 109 SER cc_start: 0.9000 (t) cc_final: 0.8768 (p) REVERT: H 110 GLU cc_start: 0.9186 (tp30) cc_final: 0.8816 (tp30) REVERT: H 117 LYS cc_start: 0.8633 (tppp) cc_final: 0.7906 (ttpp) REVERT: K 15 MET cc_start: 0.6607 (mtt) cc_final: 0.6172 (mtt) REVERT: K 16 LYS cc_start: 0.8013 (tppt) cc_final: 0.7688 (tppt) REVERT: A 42 ARG cc_start: 0.7167 (mmm-85) cc_final: 0.6600 (mmm-85) REVERT: A 90 MET cc_start: 0.8643 (mmm) cc_final: 0.8300 (mmt) REVERT: E 119 ILE cc_start: 0.9418 (pt) cc_final: 0.9170 (pt) REVERT: E 126 LEU cc_start: 0.8573 (tp) cc_final: 0.8314 (tt) outliers start: 21 outliers final: 16 residues processed: 262 average time/residue: 0.1401 time to fit residues: 50.2690 Evaluate side-chains 255 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 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 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 96 SER Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN A 39 HIS E 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097786 restraints weight = 20791.338| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.49 r_work: 0.2872 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14550 Z= 0.205 Angle : 0.682 10.709 20935 Z= 0.384 Chirality : 0.047 0.256 2347 Planarity : 0.005 0.048 1614 Dihedral : 30.169 158.566 4329 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.94 % Allowed : 22.05 % Favored : 73.00 % 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: -0.26 (0.27), residues: 913 helix: 0.73 (0.23), residues: 543 sheet: -4.39 (0.96), residues: 20 loop : -1.30 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.025 0.002 TYR F 88 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP K 21 HIS 0.034 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (14550) covalent geometry : angle 0.68225 / 0.38 (20935) hydrogen bonds : bond 0.07015 / 4.51 ( 667) hydrogen bonds : angle 3.11909 / 2.14 ( 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 291 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.321 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 77 LYS cc_start: 0.9514 (mttt) cc_final: 0.9161 (mttp) REVERT: B 82 THR cc_start: 0.9192 (p) cc_final: 0.8928 (t) REVERT: B 88 TYR cc_start: 0.9088 (m-80) cc_final: 0.8708 (m-80) REVERT: B 98 TYR cc_start: 0.9266 (m-10) cc_final: 0.8708 (m-10) REVERT: C 13 LYS cc_start: 0.7823 (tppt) cc_final: 0.7548 (tppt) REVERT: C 73 ASN cc_start: 0.7564 (t0) cc_final: 0.6795 (t0) REVERT: C 94 ASN cc_start: 0.8504 (t0) cc_final: 0.8017 (t0) REVERT: C 115 LEU cc_start: 0.8793 (mt) cc_final: 0.8592 (mp) REVERT: D 80 TYR cc_start: 0.9082 (m-10) cc_final: 0.8428 (m-10) REVERT: D 110 GLU cc_start: 0.9355 (tp30) cc_final: 0.9147 (tp30) REVERT: D 117 LYS cc_start: 0.9056 (tppp) cc_final: 0.8821 (ttmm) REVERT: D 122 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6291 (ttpp) REVERT: F 73 THR cc_start: 0.8990 (m) cc_final: 0.8690 (m) REVERT: F 74 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: F 78 ARG cc_start: 0.9108 (mtt90) cc_final: 0.8477 (mtm-85) REVERT: G 33 LEU cc_start: 0.8956 (mt) cc_final: 0.8703 (mt) REVERT: G 39 TYR cc_start: 0.9307 (m-80) cc_final: 0.9024 (m-80) REVERT: G 73 ASN cc_start: 0.8357 (t0) cc_final: 0.8063 (t0) REVERT: G 74 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8556 (mmmm) REVERT: H 31 LYS cc_start: 0.8698 (mppt) cc_final: 0.8445 (mppt) REVERT: H 57 SER cc_start: 0.8838 (m) cc_final: 0.8405 (t) REVERT: H 65 ASP cc_start: 0.9009 (t0) cc_final: 0.8776 (t0) REVERT: H 68 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8594 (mm-30) REVERT: H 80 TYR cc_start: 0.8784 (m-80) cc_final: 0.8556 (m-80) REVERT: H 84 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8337 (p) REVERT: H 109 SER cc_start: 0.9026 (t) cc_final: 0.8816 (p) REVERT: H 117 LYS cc_start: 0.8632 (tppp) cc_final: 0.8010 (ttpp) REVERT: K 14 LYS cc_start: 0.6724 (tppt) cc_final: 0.5196 (pttt) REVERT: K 16 LYS cc_start: 0.8180 (tppt) cc_final: 0.7220 (tppt) REVERT: A 39 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8069 (p-80) REVERT: A 42 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6726 (mmm-85) REVERT: A 90 MET cc_start: 0.8637 (mmm) cc_final: 0.8349 (mmp) REVERT: A 108 ASN cc_start: 0.9223 (t0) cc_final: 0.8640 (t0) REVERT: A 120 MET cc_start: 0.8256 (mtp) cc_final: 0.8038 (mtm) REVERT: E 94 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8869 (mm-30) REVERT: E 105 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8791 (mm-30) REVERT: E 119 ILE cc_start: 0.9406 (pt) cc_final: 0.9045 (pt) REVERT: L 79 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5580 (pt0) outliers start: 39 outliers final: 26 residues processed: 272 average time/residue: 0.1391 time to fit residues: 51.5719 Evaluate side-chains 273 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 33 LEU 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 79 LYS 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 40 LEU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN A 39 HIS E 39 HIS E 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096595 restraints weight = 20763.627| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.46 r_work: 0.2894 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14550 Z= 0.147 Angle : 0.611 8.081 20935 Z= 0.356 Chirality : 0.044 0.243 2347 Planarity : 0.004 0.049 1614 Dihedral : 30.001 158.252 4329 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.06 % Allowed : 23.95 % Favored : 71.99 % 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: 0.15 (0.28), residues: 913 helix: 1.08 (0.23), residues: 551 sheet: -4.27 (0.95), residues: 20 loop : -1.21 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.018 0.001 TYR D 39 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 21 HIS 0.017 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (14550) covalent geometry : angle 0.61086 / 0.36 (20935) hydrogen bonds : bond 0.06158 / 3.91 ( 667) hydrogen bonds : angle 2.90932 / 1.99 ( 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 279 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.384 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 77 LYS cc_start: 0.9557 (mttt) cc_final: 0.9199 (mttp) REVERT: B 82 THR cc_start: 0.9154 (p) cc_final: 0.8936 (t) REVERT: B 88 TYR cc_start: 0.9158 (m-10) cc_final: 0.8834 (m-80) REVERT: B 98 TYR cc_start: 0.9258 (m-10) cc_final: 0.8644 (m-10) REVERT: C 13 LYS cc_start: 0.7843 (tppt) cc_final: 0.7611 (tppt) REVERT: C 73 ASN cc_start: 0.7598 (t0) cc_final: 0.6917 (t0) REVERT: C 94 ASN cc_start: 0.8526 (t0) cc_final: 0.8008 (t0) REVERT: C 100 VAL cc_start: 0.9623 (OUTLIER) cc_final: 0.9351 (p) REVERT: D 80 TYR cc_start: 0.9018 (m-10) cc_final: 0.8350 (m-10) REVERT: D 117 LYS cc_start: 0.9089 (tppp) cc_final: 0.8860 (ttmm) REVERT: D 122 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6359 (ttpp) REVERT: F 73 THR cc_start: 0.9088 (m) cc_final: 0.8781 (m) REVERT: F 74 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: F 78 ARG cc_start: 0.9155 (mtt90) cc_final: 0.8830 (mtm-85) REVERT: F 84 MET cc_start: 0.8151 (mmt) cc_final: 0.7915 (mmt) REVERT: G 33 LEU cc_start: 0.8953 (mt) cc_final: 0.8685 (mt) REVERT: G 73 ASN cc_start: 0.8350 (t0) cc_final: 0.7792 (t0) REVERT: G 75 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8315 (mmtm) REVERT: G 110 ASN cc_start: 0.8990 (t0) cc_final: 0.8790 (t0) REVERT: H 57 SER cc_start: 0.8949 (m) cc_final: 0.8558 (t) REVERT: H 65 ASP cc_start: 0.9048 (t0) cc_final: 0.8767 (t0) REVERT: H 68 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8618 (mm-30) REVERT: H 80 TYR cc_start: 0.8798 (m-80) cc_final: 0.8404 (m-80) REVERT: H 84 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8427 (p) REVERT: H 117 LYS cc_start: 0.8674 (tppp) cc_final: 0.8040 (ttpp) REVERT: K 16 LYS cc_start: 0.8145 (tppt) cc_final: 0.7418 (tppt) REVERT: A 39 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.6915 (p-80) REVERT: A 42 ARG cc_start: 0.7277 (mmm-85) cc_final: 0.7073 (mmm-85) REVERT: A 90 MET cc_start: 0.8588 (mmm) cc_final: 0.8309 (mmt) REVERT: A 108 ASN cc_start: 0.9146 (t0) cc_final: 0.8602 (t0) REVERT: A 120 MET cc_start: 0.8227 (mtp) cc_final: 0.7984 (mtp) REVERT: E 73 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8363 (tt0) REVERT: E 76 GLN cc_start: 0.9152 (tp40) cc_final: 0.8945 (mm-40) REVERT: E 105 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9002 (mm-30) REVERT: L 79 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5573 (pt0) outliers start: 32 outliers final: 19 residues processed: 265 average time/residue: 0.1364 time to fit residues: 49.9077 Evaluate side-chains 260 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 THR 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 107 VAL Chi-restraints excluded: chain G residue 115 LEU 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 58 ILE 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 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 109 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 25 ASN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096526 restraints weight = 20660.600| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.46 r_work: 0.2897 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14550 Z= 0.139 Angle : 0.611 9.250 20935 Z= 0.353 Chirality : 0.043 0.245 2347 Planarity : 0.004 0.046 1614 Dihedral : 29.940 157.712 4329 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.82 % Allowed : 23.70 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 913 helix: 1.37 (0.23), residues: 553 sheet: -4.17 (0.93), residues: 20 loop : -1.14 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.017 0.001 TYR D 39 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP K 21 HIS 0.013 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (14550) covalent geometry : angle 0.61096 / 0.35 (20935) hydrogen bonds : bond 0.06000 / 3.83 ( 667) hydrogen bonds : angle 2.83540 / 1.93 ( 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 287 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8799 (mm-30) REVERT: B 77 LYS cc_start: 0.9571 (mttt) cc_final: 0.9202 (mttp) REVERT: B 82 THR cc_start: 0.9158 (p) cc_final: 0.8951 (t) REVERT: B 84 MET cc_start: 0.8483 (mmt) cc_final: 0.7697 (tpp) REVERT: B 88 TYR cc_start: 0.9175 (m-10) cc_final: 0.8835 (m-80) REVERT: B 98 TYR cc_start: 0.9268 (m-10) cc_final: 0.8596 (m-10) REVERT: C 13 LYS cc_start: 0.7882 (tppt) cc_final: 0.7646 (tppt) REVERT: C 73 ASN cc_start: 0.7851 (t0) cc_final: 0.7170 (t0) REVERT: C 94 ASN cc_start: 0.8551 (t0) cc_final: 0.8015 (t0) REVERT: C 100 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9337 (p) REVERT: D 80 TYR cc_start: 0.9000 (m-10) cc_final: 0.8373 (m-10) REVERT: D 102 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7835 (mm-30) REVERT: D 105 LYS cc_start: 0.9031 (tppp) cc_final: 0.8776 (mtmm) REVERT: D 110 GLU cc_start: 0.9263 (tp30) cc_final: 0.9062 (tp30) REVERT: D 117 LYS cc_start: 0.9120 (tppp) cc_final: 0.8898 (ttmm) REVERT: F 73 THR cc_start: 0.9052 (m) cc_final: 0.8716 (m) REVERT: F 74 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: F 78 ARG cc_start: 0.9163 (mtt90) cc_final: 0.8896 (mtm-85) REVERT: G 33 LEU cc_start: 0.8929 (mt) cc_final: 0.8675 (mt) REVERT: G 73 ASN cc_start: 0.8339 (t0) cc_final: 0.7792 (t0) REVERT: G 75 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8268 (mmtm) REVERT: H 57 SER cc_start: 0.8897 (m) cc_final: 0.8480 (t) REVERT: H 65 ASP cc_start: 0.9053 (t0) cc_final: 0.8769 (t0) REVERT: H 68 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8613 (mm-30) REVERT: H 80 TYR cc_start: 0.8837 (m-80) cc_final: 0.8563 (m-80) REVERT: H 84 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8492 (p) REVERT: H 117 LYS cc_start: 0.8705 (tppp) cc_final: 0.8081 (ttpp) REVERT: K 14 LYS cc_start: 0.5842 (tppt) cc_final: 0.3682 (mmtt) REVERT: K 16 LYS cc_start: 0.8257 (tppt) cc_final: 0.8039 (tppt) REVERT: A 120 MET cc_start: 0.8220 (mtp) cc_final: 0.8007 (mtp) REVERT: E 73 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8452 (tt0) REVERT: E 76 GLN cc_start: 0.9188 (tp40) cc_final: 0.8975 (mm-40) REVERT: E 105 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8950 (mm-30) REVERT: L 79 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5584 (pt0) outliers start: 38 outliers final: 25 residues processed: 264 average time/residue: 0.1331 time to fit residues: 48.2936 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 33 LEU 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 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 83 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 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 57 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN L 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093573 restraints weight = 20572.780| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.43 r_work: 0.2847 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4870 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= 0.179 Angle : 0.643 10.926 20935 Z= 0.364 Chirality : 0.045 0.237 2347 Planarity : 0.005 0.052 1614 Dihedral : 29.993 156.399 4323 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.21 % Allowed : 23.45 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 913 helix: 1.43 (0.22), residues: 550 sheet: -4.17 (0.93), residues: 20 loop : -1.10 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.017 0.002 TYR F 98 PHE 0.016 0.001 PHE A 78 TRP 0.004 0.001 TRP K 82 HIS 0.010 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (14550) covalent geometry : angle 0.64301 / 0.36 (20935) hydrogen bonds : bond 0.06493 / 4.15 ( 667) hydrogen bonds : angle 3.04391 / 2.08 ( 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 308 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 0.352 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 77 LYS cc_start: 0.9578 (mttt) cc_final: 0.9318 (mttm) REVERT: B 84 MET cc_start: 0.8562 (mmt) cc_final: 0.7831 (tpp) REVERT: B 88 TYR cc_start: 0.9257 (m-10) cc_final: 0.8632 (m-80) REVERT: B 98 TYR cc_start: 0.9273 (m-10) cc_final: 0.8591 (m-10) REVERT: C 13 LYS cc_start: 0.8029 (tppt) cc_final: 0.7818 (tppt) REVERT: C 73 ASN cc_start: 0.8177 (t0) cc_final: 0.7398 (t0) REVERT: C 94 ASN cc_start: 0.8602 (t0) cc_final: 0.8033 (t0) REVERT: D 80 TYR cc_start: 0.9072 (m-10) cc_final: 0.8281 (m-10) REVERT: D 102 GLU cc_start: 0.8033 (mm-30) cc_final: 0.6998 (mm-30) REVERT: D 105 LYS cc_start: 0.9076 (tppp) cc_final: 0.8783 (mtmm) REVERT: F 24 ASP cc_start: 0.8518 (t0) cc_final: 0.8052 (p0) REVERT: F 73 THR cc_start: 0.9107 (m) cc_final: 0.8813 (m) REVERT: F 74 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: F 78 ARG cc_start: 0.9226 (mtt90) cc_final: 0.8958 (mtm-85) REVERT: G 33 LEU cc_start: 0.9021 (mt) cc_final: 0.8778 (mt) REVERT: G 56 GLU cc_start: 0.8698 (tt0) cc_final: 0.8470 (tt0) REVERT: G 73 ASN cc_start: 0.8493 (t0) cc_final: 0.7786 (t0) REVERT: G 75 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8362 (mmtm) REVERT: H 57 SER cc_start: 0.9015 (m) cc_final: 0.8684 (t) REVERT: H 65 ASP cc_start: 0.9016 (t0) cc_final: 0.8724 (t0) REVERT: H 68 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8579 (mm-30) REVERT: H 77 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8749 (mp) REVERT: H 80 TYR cc_start: 0.8903 (m-80) cc_final: 0.8467 (m-80) REVERT: H 84 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8453 (p) REVERT: K 16 LYS cc_start: 0.8300 (tppt) cc_final: 0.8082 (tppt) REVERT: A 82 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 85 GLN cc_start: 0.8748 (mt0) cc_final: 0.8499 (mt0) REVERT: A 108 ASN cc_start: 0.8993 (t0) cc_final: 0.8586 (t0) REVERT: A 120 MET cc_start: 0.8303 (mtp) cc_final: 0.8096 (mtp) REVERT: E 41 TYR cc_start: 0.8924 (m-10) cc_final: 0.8539 (m-10) REVERT: E 45 THR cc_start: 0.8843 (t) cc_final: 0.8543 (p) REVERT: E 76 GLN cc_start: 0.9201 (tp40) cc_final: 0.8891 (mm-40) REVERT: E 105 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.9029 (mm-30) REVERT: L 79 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5733 (pt0) outliers start: 49 outliers final: 35 residues processed: 280 average time/residue: 0.1410 time to fit residues: 54.0695 Evaluate side-chains 294 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 87 VAL 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 85 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 68 ASN Chi-restraints excluded: chain G residue 83 LEU 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 77 LEU 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 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 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 23 optimal weight: 0.0070 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS 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 = 0.3939 r_free = 0.3939 target = 0.159214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095463 restraints weight = 20286.527| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.43 r_work: 0.2876 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14550 Z= 0.141 Angle : 0.609 8.520 20935 Z= 0.351 Chirality : 0.043 0.237 2347 Planarity : 0.004 0.057 1614 Dihedral : 29.834 156.679 4323 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.31 % Allowed : 26.49 % Favored : 69.20 % 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: 0.87 (0.28), residues: 913 helix: 1.71 (0.23), residues: 553 sheet: -4.09 (0.95), residues: 20 loop : -1.03 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.019 0.001 TYR F 98 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (14550) covalent geometry : angle 0.60940 / 0.35 (20935) hydrogen bonds : bond 0.05846 / 3.74 ( 667) hydrogen bonds : angle 2.83041 / 1.92 ( 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 291 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.368 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 77 LYS cc_start: 0.9585 (mttt) cc_final: 0.9287 (mttm) REVERT: B 84 MET cc_start: 0.8548 (mmt) cc_final: 0.7825 (tpp) REVERT: B 88 TYR cc_start: 0.9197 (m-10) cc_final: 0.8663 (m-80) REVERT: B 98 TYR cc_start: 0.9244 (m-10) cc_final: 0.8585 (m-10) REVERT: C 13 LYS cc_start: 0.8163 (tppt) cc_final: 0.7939 (tppt) REVERT: C 73 ASN cc_start: 0.8147 (t0) cc_final: 0.7363 (t0) REVERT: C 94 ASN cc_start: 0.8608 (t0) cc_final: 0.8016 (t0) REVERT: C 100 VAL cc_start: 0.9486 (t) cc_final: 0.9084 (p) REVERT: D 80 TYR cc_start: 0.8988 (m-10) cc_final: 0.8271 (m-10) REVERT: D 102 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 105 LYS cc_start: 0.9077 (tppp) cc_final: 0.8800 (mtmm) REVERT: F 73 THR cc_start: 0.9108 (m) cc_final: 0.8806 (m) REVERT: F 74 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: F 78 ARG cc_start: 0.9205 (mtt90) cc_final: 0.8997 (mtm-85) REVERT: G 33 LEU cc_start: 0.8983 (mt) cc_final: 0.8723 (mt) REVERT: G 73 ASN cc_start: 0.8492 (t0) cc_final: 0.7794 (t0) REVERT: G 75 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8353 (mmtm) REVERT: H 57 SER cc_start: 0.9046 (m) cc_final: 0.8716 (t) REVERT: H 65 ASP cc_start: 0.9037 (t0) cc_final: 0.8758 (t0) REVERT: H 68 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8622 (mm-30) REVERT: H 80 TYR cc_start: 0.8879 (m-80) cc_final: 0.8425 (m-80) REVERT: H 84 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8486 (p) REVERT: H 117 LYS cc_start: 0.8716 (tppp) cc_final: 0.8114 (ttpp) REVERT: K 14 LYS cc_start: 0.6009 (tppt) cc_final: 0.3786 (mmtt) REVERT: K 16 LYS cc_start: 0.8219 (tppt) cc_final: 0.7984 (tppt) REVERT: A 42 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7114 (mmm160) REVERT: A 85 GLN cc_start: 0.8891 (mt0) cc_final: 0.8560 (mt0) REVERT: A 120 MET cc_start: 0.8257 (mtp) cc_final: 0.8054 (mtp) REVERT: E 45 THR cc_start: 0.8803 (t) cc_final: 0.8553 (p) REVERT: E 76 GLN cc_start: 0.9193 (tp40) cc_final: 0.8886 (mm-40) REVERT: E 105 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9084 (mm-30) REVERT: L 79 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5743 (pt0) outliers start: 34 outliers final: 27 residues processed: 271 average time/residue: 0.1366 time to fit residues: 50.5841 Evaluate side-chains 284 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU 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 120 SER Chi-restraints excluded: chain F residue 63 GLU 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 83 LEU Chi-restraints excluded: chain G residue 91 GLU 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 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 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 105 GLU 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: 10.0000 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 39 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.157671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092893 restraints weight = 20569.982| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.50 r_work: 0.2843 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14550 Z= 0.183 Angle : 0.644 7.992 20935 Z= 0.364 Chirality : 0.044 0.247 2347 Planarity : 0.005 0.055 1614 Dihedral : 29.866 156.126 4323 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.45 % Allowed : 25.48 % Favored : 69.07 % 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: 0.86 (0.28), residues: 913 helix: 1.76 (0.23), residues: 549 sheet: -4.03 (0.96), residues: 20 loop : -1.13 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.026 0.002 TYR E 41 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP K 82 HIS 0.016 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (14550) covalent geometry : angle 0.64447 / 0.36 (20935) hydrogen bonds : bond 0.06199 / 3.98 ( 667) hydrogen bonds : angle 2.93518 / 2.00 ( 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 297 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.369 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 77 LYS cc_start: 0.9595 (mttt) cc_final: 0.9367 (mttm) REVERT: B 84 MET cc_start: 0.8577 (mmt) cc_final: 0.7855 (tpp) REVERT: B 88 TYR cc_start: 0.9218 (m-10) cc_final: 0.8730 (m-80) REVERT: B 98 TYR cc_start: 0.9273 (m-10) cc_final: 0.8588 (m-10) REVERT: C 73 ASN cc_start: 0.8220 (t0) cc_final: 0.7441 (t0) REVERT: C 100 VAL cc_start: 0.9462 (t) cc_final: 0.9042 (p) REVERT: D 80 TYR cc_start: 0.9019 (m-10) cc_final: 0.8335 (m-10) REVERT: D 102 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 105 LYS cc_start: 0.9086 (tppp) cc_final: 0.8778 (mtmm) REVERT: F 73 THR cc_start: 0.9117 (m) cc_final: 0.8821 (m) REVERT: F 74 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: F 78 ARG cc_start: 0.9231 (mtt90) cc_final: 0.9003 (mtm-85) REVERT: G 33 LEU cc_start: 0.8977 (mt) cc_final: 0.8732 (mt) REVERT: G 73 ASN cc_start: 0.8538 (t0) cc_final: 0.8084 (t0) REVERT: H 57 SER cc_start: 0.9058 (m) cc_final: 0.8734 (t) REVERT: H 65 ASP cc_start: 0.9032 (t0) cc_final: 0.8755 (t0) REVERT: H 68 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8642 (mm-30) REVERT: H 77 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8655 (mp) REVERT: H 80 TYR cc_start: 0.8872 (m-80) cc_final: 0.8366 (m-80) REVERT: H 84 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8519 (p) REVERT: K 14 LYS cc_start: 0.6037 (tppt) cc_final: 0.3813 (mmtt) REVERT: K 16 LYS cc_start: 0.8309 (tppt) cc_final: 0.8069 (tppt) REVERT: A 42 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7089 (mmm160) REVERT: A 108 ASN cc_start: 0.9149 (t0) cc_final: 0.8558 (t0) REVERT: A 120 MET cc_start: 0.8318 (mtp) cc_final: 0.8095 (mtp) REVERT: E 45 THR cc_start: 0.8846 (t) cc_final: 0.8574 (p) REVERT: E 54 TYR cc_start: 0.8863 (m-80) cc_final: 0.8610 (m-80) REVERT: E 76 GLN cc_start: 0.9223 (tp40) cc_final: 0.8923 (mm-40) REVERT: E 105 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.9047 (mm-30) REVERT: L 79 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5728 (pt0) outliers start: 43 outliers final: 34 residues processed: 272 average time/residue: 0.1480 time to fit residues: 54.9814 Evaluate side-chains 289 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU 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 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU 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 77 LEU 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 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR 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 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: 0.7980 chunk 117 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.0030 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 39 HIS E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091132 restraints weight = 20993.139| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.75 r_work: 0.2820 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14550 Z= 0.137 Angle : 0.611 9.474 20935 Z= 0.352 Chirality : 0.042 0.234 2347 Planarity : 0.004 0.054 1614 Dihedral : 29.707 156.223 4323 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.31 % Allowed : 26.87 % Favored : 68.82 % 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: 1.13 (0.28), residues: 913 helix: 2.00 (0.23), residues: 549 sheet: -3.93 (0.96), residues: 20 loop : -1.05 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 71 TYR 0.016 0.001 TYR H 37 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP K 82 HIS 0.010 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (14550) covalent geometry : angle 0.61078 / 0.35 (20935) hydrogen bonds : bond 0.05640 / 3.61 ( 667) hydrogen bonds : angle 2.75157 / 1.86 ( 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 293 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.360 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 77 LYS cc_start: 0.9491 (mttt) cc_final: 0.9223 (mttm) REVERT: B 84 MET cc_start: 0.8293 (mmt) cc_final: 0.7557 (tpp) REVERT: B 88 TYR cc_start: 0.9081 (m-10) cc_final: 0.8691 (m-80) REVERT: B 98 TYR cc_start: 0.9176 (m-10) cc_final: 0.8538 (m-10) REVERT: C 73 ASN cc_start: 0.7877 (t0) cc_final: 0.7184 (t0) REVERT: C 100 VAL cc_start: 0.9412 (t) cc_final: 0.8871 (p) REVERT: D 80 TYR cc_start: 0.8790 (m-10) cc_final: 0.8221 (m-10) REVERT: D 102 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 105 LYS cc_start: 0.8941 (tppp) cc_final: 0.8604 (mppt) REVERT: F 39 ARG cc_start: 0.8610 (mmt90) cc_final: 0.8341 (tpp-160) REVERT: F 73 THR cc_start: 0.9016 (m) cc_final: 0.8698 (m) REVERT: F 78 ARG cc_start: 0.9131 (mtt90) cc_final: 0.8878 (mtm-85) REVERT: G 33 LEU cc_start: 0.8783 (mt) cc_final: 0.8581 (mt) REVERT: G 112 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7733 (mm110) REVERT: H 57 SER cc_start: 0.8830 (m) cc_final: 0.8504 (t) REVERT: H 65 ASP cc_start: 0.8922 (t0) cc_final: 0.8641 (t0) REVERT: H 68 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8593 (mm-30) REVERT: H 80 TYR cc_start: 0.8704 (m-80) cc_final: 0.8171 (m-80) REVERT: H 84 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8165 (p) REVERT: H 117 LYS cc_start: 0.8473 (tppp) cc_final: 0.7860 (ttpp) REVERT: K 14 LYS cc_start: 0.6006 (tppt) cc_final: 0.3823 (mmtt) REVERT: A 42 ARG cc_start: 0.7072 (mmm-85) cc_final: 0.6657 (mmm160) REVERT: A 73 GLU cc_start: 0.9212 (tp30) cc_final: 0.8803 (tp30) REVERT: A 85 GLN cc_start: 0.8656 (mt0) cc_final: 0.8267 (mt0) REVERT: A 90 MET cc_start: 0.8286 (mmp) cc_final: 0.8066 (mmt) REVERT: A 120 MET cc_start: 0.7992 (mtp) cc_final: 0.7756 (mtp) REVERT: E 45 THR cc_start: 0.8625 (t) cc_final: 0.8335 (p) REVERT: E 54 TYR cc_start: 0.8515 (m-80) cc_final: 0.8253 (m-80) REVERT: E 76 GLN cc_start: 0.9133 (tp40) cc_final: 0.8867 (mm-40) REVERT: E 105 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.9016 (mm-30) REVERT: E 108 ASN cc_start: 0.9136 (t0) cc_final: 0.8841 (t0) REVERT: L 79 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5693 (pt0) outliers start: 34 outliers final: 26 residues processed: 272 average time/residue: 0.1450 time to fit residues: 53.8005 Evaluate side-chains 282 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU 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 120 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 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 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 58 THR Chi-restraints excluded: chain A residue 65 LEU 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 74 ILE Chi-restraints excluded: chain E residue 105 GLU 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: 20.0000 chunk 4 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.086893 restraints weight = 21133.285| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.74 r_work: 0.2756 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14550 Z= 0.248 Angle : 0.703 8.558 20935 Z= 0.386 Chirality : 0.046 0.235 2347 Planarity : 0.005 0.048 1614 Dihedral : 29.902 154.919 4323 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.44 % Allowed : 27.00 % Favored : 68.57 % 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: 1.68 (0.22), residues: 553 sheet: -3.83 (0.97), residues: 20 loop : -1.08 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 40 TYR 0.024 0.002 TYR F 98 PHE 0.013 0.001 PHE F 100 TRP 0.003 0.001 TRP K 21 HIS 0.027 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (14550) covalent geometry : angle 0.70258 / 0.39 (20935) hydrogen bonds : bond 0.06795 / 4.37 ( 667) hydrogen bonds : angle 3.12539 / 2.13 ( 1658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.45 seconds wall clock time: 57 minutes 10.38 seconds (3430.38 seconds total)