Starting phenix.real_space_refine on Fri Jul 3 06:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbq_16549/07_2026/8cbq_16549.map" } resolution = 4.0 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= 0.021 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 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 12959 Number of models: 1 Model: "" Number of chains: 11 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} Time building chain proxies: 2.60, per 1000 atoms: 0.20 Number of scatterers: 12959 At special positions: 0 Unit cell: (135.792, 81.144, 120.888, 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 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 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: 0.91 Conformation dependent library (CDL) restraints added in 354.6 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 63.0% alpha, 4.2% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.92 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: 3.791A 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: 3.868A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.646A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.515A 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: 3.541A 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: 3.585A 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: 3.735A 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: 3.542A 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: 3.525A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.764A 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: 3.944A 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: 3.749A 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: 3.656A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.515A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.516A 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: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.585A 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: 3.957A 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: 3.733A 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: 5.136A 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: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.571A 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: 3.622A 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: 3.683A 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: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.152A 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: 6.433A 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: 7.167A 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) 351 hydrogen bonds defined for protein. 1035 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: 2.46 Time building geometry restraints manager: 1.27 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: 2280 1.33 - 1.45: 4689 1.45 - 1.57: 6221 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 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 2.41e+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 1.29e+01 bond pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" C3' DG J -6 " pdb=" O3' DG J -6 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.13e+01 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18393 1.60 - 3.20: 1475 3.20 - 4.79: 54 4.79 - 6.39: 14 6.39 - 7.99: 7 Bond angle restraints: 19943 Sorted by residual: angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT J 13 " pdb=" C4 DT J 13 " pdb=" O4 DT J 13 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT I 55 " pdb=" C4 DT I 55 " pdb=" O4 DT I 55 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I -71 " pdb=" C4 DT I -71 " pdb=" O4 DT I -71 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6151 34.28 - 68.56: 1376 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.39: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 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 48.61 171.39 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 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1210 0.041 - 0.082: 762 0.082 - 0.123: 221 0.123 - 0.164: 56 0.164 - 0.205: 4 Chirality restraints: 2253 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 -2.53 -0.20 2.00e-01 2.50e+01 1.05e+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 9.80e-01 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 8.60e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO E 66 " 0.119 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 C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+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 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+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 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3125 2.81 - 3.33: 10148 3.33 - 3.85: 23925 3.85 - 4.38: 31341 4.38 - 4.90: 43637 Nonbonded interactions: 112176 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 3.040 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.330 3.120 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.359 3.120 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN B 25 " pdb=" OE1 GLU A 73 " model vdw 2.364 3.120 ... (remaining 112171 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.380 Find NCS groups from input model: 0.120 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 13814 Z= 0.720 Angle : 0.851 7.992 19943 Z= 0.700 Chirality : 0.054 0.205 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.198 171.394 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % 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: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 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 G 25 TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.72 (13814) covalent geometry : angle 0.85113 / 0.70 (19943) hydrogen bonds : bond 0.31386 / 20.75 ( 658) hydrogen bonds : angle 10.64236 / 7.25 ( 1637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 460 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8026 (mt) cc_final: 0.7415 (mt) REVERT: B 44 LYS cc_start: 0.8631 (tttt) cc_final: 0.8380 (mtmt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7386 (tp30) REVERT: C 32 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6706 (ttp80) REVERT: C 62 ILE cc_start: 0.9381 (mt) cc_final: 0.9068 (mm) REVERT: C 68 ASN cc_start: 0.8832 (m-40) cc_final: 0.8231 (m-40) REVERT: C 83 LEU cc_start: 0.9336 (mt) cc_final: 0.8972 (mt) REVERT: C 87 VAL cc_start: 0.9403 (m) cc_final: 0.9124 (m) REVERT: C 110 ASN cc_start: 0.7942 (t0) cc_final: 0.7375 (t0) REVERT: D 49 THR cc_start: 0.8903 (m) cc_final: 0.8702 (m) REVERT: D 59 MET cc_start: 0.8965 (mmm) cc_final: 0.8372 (tpp) REVERT: D 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7295 (mt-10) REVERT: F 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.7814 (m110) REVERT: F 34 ILE cc_start: 0.8857 (mt) cc_final: 0.8633 (mm) REVERT: F 39 ARG cc_start: 0.9036 (mmt-90) cc_final: 0.8787 (mmt180) REVERT: F 75 HIS cc_start: 0.7838 (t70) cc_final: 0.7611 (t70) REVERT: F 88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8428 (m-80) REVERT: G 20 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7420 (mtt90) REVERT: G 57 TYR cc_start: 0.8128 (t80) cc_final: 0.7804 (t80) REVERT: G 110 ASN cc_start: 0.8643 (t0) cc_final: 0.8246 (t0) REVERT: H 110 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 113 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8240 (tppt) REVERT: K 40 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2391 (tp) REVERT: A 46 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 49 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7531 (mtp-110) REVERT: A 51 ILE cc_start: 0.8963 (mt) cc_final: 0.8737 (mt) REVERT: A 55 GLN cc_start: 0.8344 (mt0) cc_final: 0.7895 (mt0) REVERT: A 62 ILE cc_start: 0.8573 (mt) cc_final: 0.8240 (mt) REVERT: A 76 GLN cc_start: 0.8258 (mm110) cc_final: 0.7928 (mm-40) REVERT: A 84 PHE cc_start: 0.8420 (m-80) cc_final: 0.7629 (m-80) REVERT: A 99 TYR cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: A 120 MET cc_start: 0.7237 (mtp) cc_final: 0.6922 (mmm) REVERT: E 60 LEU cc_start: 0.8200 (mt) cc_final: 0.7431 (mp) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9191 (t) REVERT: E 74 ILE cc_start: 0.9177 (mt) cc_final: 0.8909 (tt) REVERT: E 117 VAL cc_start: 0.9086 (t) cc_final: 0.8853 (p) REVERT: E 118 THR cc_start: 0.8515 (m) cc_final: 0.7808 (p) REVERT: E 119 ILE cc_start: 0.8810 (pt) cc_final: 0.7799 (pt) REVERT: E 120 MET cc_start: 0.7605 (mtt) cc_final: 0.6556 (mpp) outliers start: 13 outliers final: 6 residues processed: 468 average time/residue: 0.1556 time to fit residues: 94.2603 Evaluate side-chains 374 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 366 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 64 ASN D 46 HIS F 18 HIS G 89 ASN H 64 ASN K 64 ASN K 86 ASN A 85 GLN A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.149648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108161 restraints weight = 28642.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111744 restraints weight = 14852.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114094 restraints weight = 9840.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115589 restraints weight = 7598.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116524 restraints weight = 6509.666| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 13814 Z= 0.204 Angle : 0.869 8.419 19943 Z= 0.480 Chirality : 0.053 0.278 2253 Planarity : 0.008 0.083 1485 Dihedral : 30.000 167.585 4250 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.05 % Allowed : 22.86 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.24), residues: 831 helix: -1.96 (0.18), residues: 525 sheet: -3.97 (1.04), residues: 17 loop : -1.45 (0.30), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 55 TYR 0.034 0.003 TYR B 88 PHE 0.025 0.002 PHE A 78 TRP 0.003 0.001 TRP K 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (13814) covalent geometry : angle 0.86901 / 0.48 (19943) hydrogen bonds : bond 0.08465 / 5.47 ( 658) hydrogen bonds : angle 3.84840 / 2.59 ( 1637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 398 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8702 (m110) cc_final: 0.8316 (m-40) REVERT: B 53 GLU cc_start: 0.8356 (tp30) cc_final: 0.7899 (tp30) REVERT: B 79 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8430 (mmtm) REVERT: C 56 GLU cc_start: 0.8660 (tt0) cc_final: 0.7837 (tt0) REVERT: C 71 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7140 (ttp-110) REVERT: C 73 ASN cc_start: 0.8706 (m-40) cc_final: 0.8295 (m-40) REVERT: C 75 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8286 (mmmm) REVERT: C 92 GLU cc_start: 0.8425 (mp0) cc_final: 0.8205 (mm-30) REVERT: C 95 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8578 (pttt) REVERT: C 110 ASN cc_start: 0.8762 (t0) cc_final: 0.8274 (t0) REVERT: D 43 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8944 (tppt) REVERT: D 64 ASN cc_start: 0.8669 (m110) cc_final: 0.8150 (m110) REVERT: D 65 ASP cc_start: 0.8627 (t70) cc_final: 0.8237 (t70) REVERT: D 105 LYS cc_start: 0.8541 (tptp) cc_final: 0.8326 (tptp) REVERT: D 110 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 113 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8837 (mmtm) REVERT: D 117 LYS cc_start: 0.9329 (tttt) cc_final: 0.9067 (pttp) REVERT: F 25 ASN cc_start: 0.8557 (m-40) cc_final: 0.7976 (m-40) REVERT: F 39 ARG cc_start: 0.9222 (mmt-90) cc_final: 0.8922 (mmt180) REVERT: F 51 TYR cc_start: 0.7881 (m-10) cc_final: 0.7535 (m-10) REVERT: F 53 GLU cc_start: 0.8628 (tp30) cc_final: 0.8182 (tp30) REVERT: F 75 HIS cc_start: 0.8107 (t70) cc_final: 0.7602 (t70) REVERT: F 88 TYR cc_start: 0.9288 (m-10) cc_final: 0.8798 (m-80) REVERT: G 17 ARG cc_start: 0.8343 (mtm180) cc_final: 0.7686 (ptp-170) REVERT: G 32 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8322 (ttp80) REVERT: G 42 ARG cc_start: 0.8508 (mtp-110) cc_final: 0.8172 (mtm-85) REVERT: G 61 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8281 (mm-30) REVERT: G 68 ASN cc_start: 0.8569 (p0) cc_final: 0.8228 (p0) REVERT: G 73 ASN cc_start: 0.8924 (t0) cc_final: 0.8460 (t0) REVERT: G 81 ARG cc_start: 0.8341 (tpt90) cc_final: 0.8077 (tpt90) REVERT: G 92 GLU cc_start: 0.8590 (pm20) cc_final: 0.8173 (pm20) REVERT: G 110 ASN cc_start: 0.8861 (t0) cc_final: 0.8408 (t0) REVERT: H 40 LYS cc_start: 0.8993 (tppt) cc_final: 0.8463 (tppt) REVERT: H 43 LYS cc_start: 0.8616 (pptt) cc_final: 0.7804 (pptt) REVERT: H 44 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8036 (mm-40) REVERT: H 49 THR cc_start: 0.9052 (p) cc_final: 0.8835 (p) REVERT: H 73 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8703 (mm-30) REVERT: H 102 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8509 (mm-30) REVERT: H 110 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8441 (tt0) REVERT: H 113 LYS cc_start: 0.9328 (mtmt) cc_final: 0.8961 (ptpt) REVERT: K 40 LEU cc_start: 0.3407 (OUTLIER) cc_final: 0.3040 (tp) REVERT: A 55 GLN cc_start: 0.9071 (mt0) cc_final: 0.8524 (tt0) REVERT: A 56 LYS cc_start: 0.8464 (pttp) cc_final: 0.8142 (ptpp) REVERT: A 76 GLN cc_start: 0.8708 (mm110) cc_final: 0.8172 (mm-40) REVERT: A 79 LYS cc_start: 0.8743 (tptp) cc_final: 0.8127 (tptp) REVERT: A 106 ASP cc_start: 0.8659 (m-30) cc_final: 0.8360 (m-30) REVERT: A 129 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8144 (mmp80) REVERT: E 41 TYR cc_start: 0.7998 (m-80) cc_final: 0.7673 (m-80) REVERT: E 49 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7962 (ptp-170) REVERT: E 54 TYR cc_start: 0.7872 (m-10) cc_final: 0.7642 (m-10) REVERT: E 60 LEU cc_start: 0.9131 (mt) cc_final: 0.8874 (mm) REVERT: E 67 PHE cc_start: 0.8547 (t80) cc_final: 0.7643 (t80) REVERT: E 71 VAL cc_start: 0.9133 (t) cc_final: 0.8822 (t) REVERT: E 85 GLN cc_start: 0.8007 (mt0) cc_final: 0.7532 (mt0) REVERT: E 93 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7766 (tm-30) REVERT: E 105 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7414 (tm-30) REVERT: E 117 VAL cc_start: 0.9151 (t) cc_final: 0.8867 (p) REVERT: E 125 GLN cc_start: 0.8705 (mt0) cc_final: 0.8423 (mm-40) outliers start: 36 outliers final: 25 residues processed: 413 average time/residue: 0.1467 time to fit residues: 80.0745 Evaluate side-chains 395 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN G 89 ASN H 46 HIS H 92 GLN H 106 HIS A 85 GLN A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.144436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101261 restraints weight = 29255.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104697 restraints weight = 15322.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106925 restraints weight = 10258.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108341 restraints weight = 7999.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109248 restraints weight = 6890.723| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13814 Z= 0.187 Angle : 0.768 9.651 19943 Z= 0.432 Chirality : 0.049 0.255 2253 Planarity : 0.007 0.074 1485 Dihedral : 30.232 164.010 4249 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.59 % Allowed : 26.65 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.27), residues: 831 helix: -0.36 (0.21), residues: 528 sheet: -4.10 (1.34), residues: 10 loop : -1.10 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 129 TYR 0.022 0.002 TYR G 39 PHE 0.015 0.002 PHE F 61 TRP 0.004 0.001 TRP K 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (13814) covalent geometry : angle 0.76757 / 0.43 (19943) hydrogen bonds : bond 0.07081 / 4.54 ( 658) hydrogen bonds : angle 3.52159 / 2.38 ( 1637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 390 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8666 (mtp-110) cc_final: 0.8404 (ttt90) REVERT: B 53 GLU cc_start: 0.8467 (tp30) cc_final: 0.8178 (tp30) REVERT: B 79 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8622 (mmtp) REVERT: C 17 ARG cc_start: 0.8873 (mtm180) cc_final: 0.8339 (ptp-170) REVERT: C 32 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7251 (ttp-110) REVERT: C 56 GLU cc_start: 0.8581 (tt0) cc_final: 0.8305 (tt0) REVERT: C 71 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7413 (ttp-110) REVERT: C 75 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8343 (mmmm) REVERT: C 91 GLU cc_start: 0.8162 (pm20) cc_final: 0.7626 (pm20) REVERT: C 95 LYS cc_start: 0.9144 (ptpt) cc_final: 0.8700 (pttt) REVERT: C 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8422 (t0) REVERT: D 59 MET cc_start: 0.9732 (mmm) cc_final: 0.9273 (tpp) REVERT: D 65 ASP cc_start: 0.8840 (t70) cc_final: 0.8419 (t70) REVERT: D 92 GLN cc_start: 0.8288 (pt0) cc_final: 0.7755 (pp30) REVERT: D 102 GLU cc_start: 0.7979 (tp30) cc_final: 0.7697 (tp30) REVERT: D 110 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7715 (mt-10) REVERT: D 113 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8828 (mmtm) REVERT: F 25 ASN cc_start: 0.8544 (m-40) cc_final: 0.8140 (m-40) REVERT: F 51 TYR cc_start: 0.8237 (m-80) cc_final: 0.7693 (m-80) REVERT: F 53 GLU cc_start: 0.8639 (tp30) cc_final: 0.8177 (tp30) REVERT: F 75 HIS cc_start: 0.8085 (t70) cc_final: 0.7445 (t70) REVERT: F 78 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7985 (tpp80) REVERT: F 88 TYR cc_start: 0.9298 (m-10) cc_final: 0.8706 (m-80) REVERT: F 92 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8583 (mmm-85) REVERT: G 17 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7377 (ptp-170) REVERT: G 35 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7437 (mmp80) REVERT: G 42 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.8174 (mtm110) REVERT: G 61 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8097 (mm-30) REVERT: G 68 ASN cc_start: 0.8385 (p0) cc_final: 0.7853 (p0) REVERT: G 72 ASP cc_start: 0.7784 (m-30) cc_final: 0.7465 (m-30) REVERT: G 73 ASN cc_start: 0.8376 (t0) cc_final: 0.8140 (t0) REVERT: G 81 ARG cc_start: 0.8578 (tpt90) cc_final: 0.8254 (tpt90) REVERT: G 95 LYS cc_start: 0.9083 (pttp) cc_final: 0.8543 (pttm) REVERT: G 110 ASN cc_start: 0.8968 (t0) cc_final: 0.8539 (t0) REVERT: H 34 TYR cc_start: 0.8082 (m-80) cc_final: 0.7720 (m-80) REVERT: H 39 TYR cc_start: 0.8351 (t80) cc_final: 0.8081 (t80) REVERT: H 40 LYS cc_start: 0.9472 (tppt) cc_final: 0.9085 (tppt) REVERT: H 44 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8392 (mm110) REVERT: H 56 MET cc_start: 0.8158 (tmm) cc_final: 0.7904 (tmm) REVERT: H 59 MET cc_start: 0.8898 (mmp) cc_final: 0.8516 (mmp) REVERT: H 73 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8827 (mm-30) REVERT: H 102 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8021 (mm-30) REVERT: H 110 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8441 (tt0) REVERT: H 113 LYS cc_start: 0.9344 (mtmt) cc_final: 0.8958 (ptpt) REVERT: K 40 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3681 (tp) REVERT: A 49 ARG cc_start: 0.8537 (ttm110) cc_final: 0.8099 (mtm110) REVERT: A 55 GLN cc_start: 0.9191 (mt0) cc_final: 0.8778 (tt0) REVERT: A 56 LYS cc_start: 0.8468 (pttp) cc_final: 0.8124 (pttp) REVERT: A 76 GLN cc_start: 0.8809 (mm110) cc_final: 0.8397 (mm-40) REVERT: A 93 GLN cc_start: 0.8011 (tt0) cc_final: 0.7713 (mt0) REVERT: A 106 ASP cc_start: 0.8569 (m-30) cc_final: 0.8321 (m-30) REVERT: E 41 TYR cc_start: 0.8009 (m-80) cc_final: 0.7600 (m-80) REVERT: E 49 ARG cc_start: 0.8371 (ptm160) cc_final: 0.8029 (ptp-170) REVERT: E 67 PHE cc_start: 0.8499 (t80) cc_final: 0.7802 (t80) REVERT: E 79 LYS cc_start: 0.8116 (tppt) cc_final: 0.7838 (tppt) REVERT: E 85 GLN cc_start: 0.7985 (mt0) cc_final: 0.7285 (mt0) REVERT: E 105 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 113 HIS cc_start: 0.7659 (t70) cc_final: 0.7379 (t70) REVERT: E 117 VAL cc_start: 0.9213 (t) cc_final: 0.8938 (p) REVERT: E 120 MET cc_start: 0.6562 (mtp) cc_final: 0.6138 (mpp) REVERT: E 125 GLN cc_start: 0.8690 (mt0) cc_final: 0.8427 (mm-40) outliers start: 47 outliers final: 32 residues processed: 406 average time/residue: 0.1457 time to fit residues: 77.9368 Evaluate side-chains 407 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 122 LYS 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 74 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 64 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN A 85 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098919 restraints weight = 29507.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102195 restraints weight = 15855.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104298 restraints weight = 10829.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105603 restraints weight = 8591.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106383 restraints weight = 7489.440| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13814 Z= 0.173 Angle : 0.717 7.256 19943 Z= 0.407 Chirality : 0.046 0.266 2253 Planarity : 0.005 0.058 1485 Dihedral : 30.275 161.234 4242 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.73 % Allowed : 30.86 % Favored : 62.41 % 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: -0.45 (0.27), residues: 831 helix: 0.25 (0.22), residues: 529 sheet: -3.93 (1.38), residues: 10 loop : -1.04 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 99 TYR 0.021 0.002 TYR F 51 PHE 0.022 0.002 PHE B 61 TRP 0.003 0.001 TRP K 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (13814) covalent geometry : angle 0.71668 / 0.41 (19943) hydrogen bonds : bond 0.06355 / 4.09 ( 658) hydrogen bonds : angle 3.32429 / 2.23 ( 1637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8797 (tptp) REVERT: B 35 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8592 (mtp85) REVERT: B 45 ARG cc_start: 0.8852 (mtp-110) cc_final: 0.8583 (ttp80) REVERT: B 53 GLU cc_start: 0.8493 (tp30) cc_final: 0.8135 (tp30) REVERT: B 63 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 24 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 29 ARG cc_start: 0.8859 (tpp80) cc_final: 0.8547 (tpp80) REVERT: C 32 ARG cc_start: 0.7970 (ttp80) cc_final: 0.6927 (ttp-110) REVERT: C 56 GLU cc_start: 0.8647 (tt0) cc_final: 0.8418 (tt0) REVERT: C 64 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8335 (tm-30) REVERT: C 71 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7426 (ttp-110) REVERT: C 75 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8369 (mmmm) REVERT: C 89 ASN cc_start: 0.8685 (m-40) cc_final: 0.8424 (m110) REVERT: C 92 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7957 (mm-30) REVERT: C 110 ASN cc_start: 0.9031 (t0) cc_final: 0.8689 (t0) REVERT: C 115 LEU cc_start: 0.9087 (mp) cc_final: 0.8356 (mp) REVERT: D 36 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9019 (pt) REVERT: D 59 MET cc_start: 0.9752 (mmm) cc_final: 0.9401 (tpp) REVERT: D 65 ASP cc_start: 0.8845 (t70) cc_final: 0.8561 (t70) REVERT: D 69 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8490 (mtp180) REVERT: D 92 GLN cc_start: 0.8231 (pt0) cc_final: 0.7679 (pp30) REVERT: D 109 SER cc_start: 0.9311 (t) cc_final: 0.8697 (p) REVERT: D 110 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7782 (mt-10) REVERT: D 113 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8820 (mmtm) REVERT: D 117 LYS cc_start: 0.9302 (tttt) cc_final: 0.8854 (ptmt) REVERT: F 25 ASN cc_start: 0.8588 (m-40) cc_final: 0.8326 (m-40) REVERT: F 44 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8648 (ttmm) REVERT: F 53 GLU cc_start: 0.8584 (tp30) cc_final: 0.8173 (tp30) REVERT: F 75 HIS cc_start: 0.8115 (t70) cc_final: 0.7709 (t70) REVERT: F 78 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8083 (tpp80) REVERT: F 88 TYR cc_start: 0.9287 (m-10) cc_final: 0.8803 (m-80) REVERT: F 92 ARG cc_start: 0.9007 (mmm160) cc_final: 0.8406 (mmm-85) REVERT: G 17 ARG cc_start: 0.8283 (mtm180) cc_final: 0.7538 (ptp-170) REVERT: G 42 ARG cc_start: 0.8533 (mtp-110) cc_final: 0.8157 (mtm-85) REVERT: G 61 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8228 (mm-30) REVERT: G 64 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7722 (tm-30) REVERT: G 68 ASN cc_start: 0.8457 (p0) cc_final: 0.8006 (p0) REVERT: G 72 ASP cc_start: 0.7834 (m-30) cc_final: 0.7537 (m-30) REVERT: G 78 ILE cc_start: 0.8493 (mt) cc_final: 0.8062 (mt) REVERT: G 81 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8299 (tpt90) REVERT: G 95 LYS cc_start: 0.9141 (pttp) cc_final: 0.8473 (ptpp) REVERT: H 34 TYR cc_start: 0.8198 (m-80) cc_final: 0.7493 (m-10) REVERT: H 39 TYR cc_start: 0.8366 (t80) cc_final: 0.8145 (t80) REVERT: H 40 LYS cc_start: 0.9466 (tppt) cc_final: 0.8858 (tppt) REVERT: H 44 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8277 (mm110) REVERT: H 56 MET cc_start: 0.8147 (tmm) cc_final: 0.7878 (tmm) REVERT: H 59 MET cc_start: 0.8988 (mmp) cc_final: 0.8615 (mmp) REVERT: H 68 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8378 (mm-30) REVERT: H 73 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: H 102 GLU cc_start: 0.9038 (mm-30) cc_final: 0.7980 (mm-30) REVERT: H 110 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8470 (tt0) REVERT: H 113 LYS cc_start: 0.9325 (mtmt) cc_final: 0.8981 (ptpt) REVERT: K 40 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4343 (tp) REVERT: A 49 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8223 (mtp-110) REVERT: A 56 LYS cc_start: 0.8509 (pttp) cc_final: 0.8110 (pttp) REVERT: A 74 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8993 (tp) REVERT: A 76 GLN cc_start: 0.8861 (mm110) cc_final: 0.8458 (mm-40) REVERT: A 79 LYS cc_start: 0.9041 (tptp) cc_final: 0.8838 (tptp) REVERT: A 106 ASP cc_start: 0.8494 (m-30) cc_final: 0.8230 (m-30) REVERT: E 60 LEU cc_start: 0.9261 (mt) cc_final: 0.8876 (mm) REVERT: E 67 PHE cc_start: 0.8632 (t80) cc_final: 0.7984 (t80) REVERT: E 85 GLN cc_start: 0.8101 (mt0) cc_final: 0.7477 (mt0) REVERT: E 97 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8201 (mt-10) REVERT: E 99 TYR cc_start: 0.8956 (t80) cc_final: 0.8703 (t80) REVERT: E 105 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 117 VAL cc_start: 0.9342 (t) cc_final: 0.9112 (p) REVERT: E 125 GLN cc_start: 0.8721 (mt0) cc_final: 0.8429 (mm-40) outliers start: 48 outliers final: 33 residues processed: 403 average time/residue: 0.1446 time to fit residues: 76.8047 Evaluate side-chains 418 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 381 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 64 ASN G 73 ASN A 108 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097581 restraints weight = 29810.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100789 restraints weight = 16094.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102888 restraints weight = 11053.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104218 restraints weight = 8781.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105000 restraints weight = 7642.720| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13814 Z= 0.173 Angle : 0.712 9.060 19943 Z= 0.403 Chirality : 0.046 0.258 2253 Planarity : 0.005 0.060 1485 Dihedral : 30.279 160.044 4240 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.31 % Allowed : 32.82 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 831 helix: 0.49 (0.22), residues: 529 sheet: -3.72 (1.48), residues: 10 loop : -0.93 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 69 TYR 0.024 0.002 TYR H 37 PHE 0.021 0.002 PHE F 61 TRP 0.003 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (13814) covalent geometry : angle 0.71168 / 0.40 (19943) hydrogen bonds : bond 0.06156 / 3.95 ( 658) hydrogen bonds : angle 3.32366 / 2.23 ( 1637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 35 ARG cc_start: 0.9242 (mtp85) cc_final: 0.8698 (mtp85) REVERT: B 44 LYS cc_start: 0.9285 (mttt) cc_final: 0.8795 (mttp) REVERT: B 45 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8617 (mtp85) REVERT: B 53 GLU cc_start: 0.8513 (tp30) cc_final: 0.8213 (tp30) REVERT: B 63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 24 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8027 (mm110) REVERT: C 32 ARG cc_start: 0.7854 (ttp80) cc_final: 0.6649 (ttp-170) REVERT: C 36 LYS cc_start: 0.8178 (pttm) cc_final: 0.7402 (ptpp) REVERT: C 56 GLU cc_start: 0.8674 (tt0) cc_final: 0.8467 (tt0) REVERT: C 71 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7572 (ttp-110) REVERT: C 75 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8543 (mmmm) REVERT: C 84 GLN cc_start: 0.9348 (tp-100) cc_final: 0.9123 (tp-100) REVERT: C 89 ASN cc_start: 0.8703 (m-40) cc_final: 0.8346 (m110) REVERT: C 110 ASN cc_start: 0.8994 (t0) cc_final: 0.8676 (t0) REVERT: D 36 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9052 (pt) REVERT: D 59 MET cc_start: 0.9756 (mmm) cc_final: 0.9426 (tpp) REVERT: D 65 ASP cc_start: 0.8821 (t70) cc_final: 0.8536 (t70) REVERT: D 69 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8430 (mtp180) REVERT: D 92 GLN cc_start: 0.8246 (pt0) cc_final: 0.7805 (pp30) REVERT: D 109 SER cc_start: 0.9302 (t) cc_final: 0.8713 (p) REVERT: D 110 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 113 LYS cc_start: 0.9045 (mmtm) cc_final: 0.8765 (mmtm) REVERT: D 117 LYS cc_start: 0.9301 (tttt) cc_final: 0.8964 (ptmt) REVERT: F 25 ASN cc_start: 0.8609 (m-40) cc_final: 0.8329 (m-40) REVERT: F 44 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8834 (mtmm) REVERT: F 52 GLU cc_start: 0.8937 (tp30) cc_final: 0.8647 (tp30) REVERT: F 53 GLU cc_start: 0.8614 (tp30) cc_final: 0.8222 (tp30) REVERT: F 63 GLU cc_start: 0.7644 (pp20) cc_final: 0.6607 (pp20) REVERT: F 75 HIS cc_start: 0.8197 (t70) cc_final: 0.7972 (t70) REVERT: F 78 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8293 (tpp80) REVERT: F 88 TYR cc_start: 0.9302 (m-10) cc_final: 0.8832 (m-80) REVERT: F 92 ARG cc_start: 0.8981 (mmm160) cc_final: 0.8633 (mmm-85) REVERT: G 17 ARG cc_start: 0.8565 (mtm180) cc_final: 0.7630 (ptp-170) REVERT: G 24 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7180 (mm-40) REVERT: G 39 TYR cc_start: 0.8838 (m-80) cc_final: 0.8170 (m-80) REVERT: G 42 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8225 (mtm-85) REVERT: G 61 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8139 (mm-30) REVERT: G 64 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7771 (tm-30) REVERT: G 68 ASN cc_start: 0.8396 (p0) cc_final: 0.7811 (p0) REVERT: G 72 ASP cc_start: 0.7868 (m-30) cc_final: 0.7606 (m-30) REVERT: G 78 ILE cc_start: 0.8763 (mt) cc_final: 0.8370 (mt) REVERT: G 81 ARG cc_start: 0.8646 (tpt90) cc_final: 0.8431 (tpt90) REVERT: G 95 LYS cc_start: 0.9200 (pttp) cc_final: 0.8543 (ptpp) REVERT: G 112 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8549 (mm110) REVERT: H 39 TYR cc_start: 0.8388 (t80) cc_final: 0.8183 (t80) REVERT: H 40 LYS cc_start: 0.9477 (tppt) cc_final: 0.8949 (tppt) REVERT: H 44 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8416 (mm110) REVERT: H 56 MET cc_start: 0.8202 (tmm) cc_final: 0.7924 (tmm) REVERT: H 59 MET cc_start: 0.9181 (mmp) cc_final: 0.8873 (mmp) REVERT: H 73 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8901 (mm-30) REVERT: H 102 GLU cc_start: 0.9048 (mm-30) cc_final: 0.7998 (mm-30) REVERT: H 110 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8489 (tt0) REVERT: H 113 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8981 (ptpt) REVERT: K 40 LEU cc_start: 0.4736 (OUTLIER) cc_final: 0.4338 (tp) REVERT: K 79 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: A 56 LYS cc_start: 0.8530 (pttp) cc_final: 0.8111 (pttp) REVERT: A 74 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8975 (mm) REVERT: A 76 GLN cc_start: 0.8875 (mm110) cc_final: 0.8477 (mm-40) REVERT: A 106 ASP cc_start: 0.8637 (m-30) cc_final: 0.8210 (m-30) REVERT: E 49 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8119 (ptp-170) REVERT: E 56 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7807 (mmtm) REVERT: E 60 LEU cc_start: 0.9335 (mt) cc_final: 0.8988 (mm) REVERT: E 67 PHE cc_start: 0.8748 (t80) cc_final: 0.8243 (t80) REVERT: E 68 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: E 85 GLN cc_start: 0.8224 (mt0) cc_final: 0.7536 (mt0) REVERT: E 97 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8241 (mt-10) REVERT: E 105 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 115 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8567 (mmmm) REVERT: E 117 VAL cc_start: 0.9354 (t) cc_final: 0.9115 (p) REVERT: E 120 MET cc_start: 0.6671 (mtp) cc_final: 0.6142 (mpp) outliers start: 45 outliers final: 36 residues processed: 403 average time/residue: 0.1451 time to fit residues: 77.0397 Evaluate side-chains 416 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN G 73 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.141264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096286 restraints weight = 29708.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099485 restraints weight = 16381.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101546 restraints weight = 11360.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102810 restraints weight = 9045.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103574 restraints weight = 7904.973| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13814 Z= 0.176 Angle : 0.712 9.156 19943 Z= 0.402 Chirality : 0.046 0.257 2253 Planarity : 0.006 0.088 1485 Dihedral : 30.238 159.284 4239 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 7.71 % Allowed : 33.66 % Favored : 58.63 % 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: -0.01 (0.28), residues: 831 helix: 0.59 (0.22), residues: 533 sheet: -3.69 (1.43), residues: 10 loop : -0.85 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG G 20 TYR 0.025 0.002 TYR H 37 PHE 0.016 0.001 PHE B 61 TRP 0.003 0.001 TRP K 82 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (13814) covalent geometry : angle 0.71154 / 0.40 (19943) hydrogen bonds : bond 0.06006 / 3.84 ( 658) hydrogen bonds : angle 3.30007 / 2.23 ( 1637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 385 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9254 (mtp85) cc_final: 0.8946 (mtp85) REVERT: B 39 ARG cc_start: 0.9334 (mmt-90) cc_final: 0.8949 (tpp80) REVERT: B 45 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8608 (mtp85) REVERT: B 53 GLU cc_start: 0.8494 (tp30) cc_final: 0.8177 (tp30) REVERT: B 63 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 20 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8333 (mmt-90) REVERT: C 24 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 32 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7122 (ttp-170) REVERT: C 56 GLU cc_start: 0.8653 (tt0) cc_final: 0.8444 (tt0) REVERT: C 75 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8606 (mmmm) REVERT: C 89 ASN cc_start: 0.8665 (m-40) cc_final: 0.8301 (m110) REVERT: C 92 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7030 (mm-30) REVERT: C 95 LYS cc_start: 0.8804 (ptpt) cc_final: 0.8388 (pttm) REVERT: C 110 ASN cc_start: 0.9013 (t0) cc_final: 0.8693 (t0) REVERT: D 34 TYR cc_start: 0.8325 (m-10) cc_final: 0.8073 (m-10) REVERT: D 59 MET cc_start: 0.9740 (mmm) cc_final: 0.9483 (tpp) REVERT: D 65 ASP cc_start: 0.8831 (t70) cc_final: 0.8552 (t70) REVERT: D 69 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8423 (mtp180) REVERT: D 109 SER cc_start: 0.9384 (t) cc_final: 0.8949 (p) REVERT: D 110 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8052 (mt-10) REVERT: F 75 HIS cc_start: 0.8361 (t70) cc_final: 0.8040 (t70) REVERT: F 78 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8426 (tpp80) REVERT: F 88 TYR cc_start: 0.9342 (m-10) cc_final: 0.8861 (m-80) REVERT: F 92 ARG cc_start: 0.9001 (mmm160) cc_final: 0.8700 (mmm-85) REVERT: F 95 ARG cc_start: 0.8649 (mtt90) cc_final: 0.7990 (mtt90) REVERT: G 17 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8238 (ptp-170) REVERT: G 24 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7569 (mm-40) REVERT: G 39 TYR cc_start: 0.9036 (m-80) cc_final: 0.8722 (m-80) REVERT: G 42 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8180 (mtm110) REVERT: G 61 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7972 (mm-30) REVERT: G 64 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7701 (tm-30) REVERT: G 68 ASN cc_start: 0.8386 (p0) cc_final: 0.7836 (p0) REVERT: G 72 ASP cc_start: 0.7864 (m-30) cc_final: 0.7575 (m-30) REVERT: G 78 ILE cc_start: 0.8834 (mt) cc_final: 0.8447 (mt) REVERT: G 89 ASN cc_start: 0.8596 (p0) cc_final: 0.8238 (p0) REVERT: G 95 LYS cc_start: 0.9212 (pttp) cc_final: 0.8589 (ptpp) REVERT: H 32 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7837 (tm-30) REVERT: H 39 TYR cc_start: 0.8400 (t80) cc_final: 0.8183 (t80) REVERT: H 40 LYS cc_start: 0.9387 (tppt) cc_final: 0.8890 (tppt) REVERT: H 44 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8357 (mm110) REVERT: H 56 MET cc_start: 0.8128 (tmm) cc_final: 0.7821 (tmm) REVERT: H 59 MET cc_start: 0.9217 (mmp) cc_final: 0.8931 (mmp) REVERT: H 76 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8421 (mtm-85) REVERT: H 102 GLU cc_start: 0.9026 (mm-30) cc_final: 0.7999 (mm-30) REVERT: H 110 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8503 (tt0) REVERT: H 113 LYS cc_start: 0.9338 (mtmt) cc_final: 0.8990 (ptpt) REVERT: K 40 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4389 (tp) REVERT: K 79 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: A 49 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8308 (mtm110) REVERT: A 53 ARG cc_start: 0.8693 (ttt180) cc_final: 0.8378 (tmm-80) REVERT: A 56 LYS cc_start: 0.8522 (pttp) cc_final: 0.8087 (pttp) REVERT: A 76 GLN cc_start: 0.8889 (mm110) cc_final: 0.8512 (mm-40) REVERT: A 79 LYS cc_start: 0.9068 (tptp) cc_final: 0.8836 (tptp) REVERT: A 106 ASP cc_start: 0.8525 (m-30) cc_final: 0.8161 (m-30) REVERT: E 67 PHE cc_start: 0.8719 (t80) cc_final: 0.8223 (t80) REVERT: E 79 LYS cc_start: 0.8303 (tppt) cc_final: 0.7719 (tppt) REVERT: E 82 LEU cc_start: 0.9150 (mt) cc_final: 0.8904 (mt) REVERT: E 85 GLN cc_start: 0.8122 (mt0) cc_final: 0.7423 (mt0) REVERT: E 97 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8210 (mt-10) REVERT: E 105 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7596 (tm-30) REVERT: E 108 ASN cc_start: 0.9431 (t0) cc_final: 0.9209 (t0) REVERT: E 115 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8562 (mmmm) REVERT: E 117 VAL cc_start: 0.9371 (t) cc_final: 0.9146 (p) REVERT: E 125 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7748 (mp10) outliers start: 55 outliers final: 45 residues processed: 399 average time/residue: 0.1388 time to fit residues: 73.7801 Evaluate side-chains 423 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 376 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN F 75 HIS G 73 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.141549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096774 restraints weight = 29515.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.099986 restraints weight = 16114.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102042 restraints weight = 11099.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103316 restraints weight = 8838.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104042 restraints weight = 7711.341| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13814 Z= 0.162 Angle : 0.717 9.935 19943 Z= 0.403 Chirality : 0.046 0.405 2253 Planarity : 0.006 0.084 1485 Dihedral : 30.209 158.837 4239 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.73 % Allowed : 35.62 % Favored : 57.64 % 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: 0.16 (0.28), residues: 831 helix: 0.66 (0.22), residues: 531 sheet: -3.50 (1.44), residues: 10 loop : -0.65 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 20 TYR 0.023 0.002 TYR H 37 PHE 0.027 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (13814) covalent geometry : angle 0.71663 / 0.40 (19943) hydrogen bonds : bond 0.05797 / 3.68 ( 658) hydrogen bonds : angle 3.27567 / 2.21 ( 1637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.9328 (mttt) cc_final: 0.8592 (mttt) REVERT: B 45 ARG cc_start: 0.9013 (mtp-110) cc_final: 0.8641 (mtp85) REVERT: B 53 GLU cc_start: 0.8477 (tp30) cc_final: 0.8106 (tp30) REVERT: B 63 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7734 (mt-10) REVERT: C 17 ARG cc_start: 0.8869 (mtm180) cc_final: 0.8463 (mtt90) REVERT: C 20 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.8515 (mmt-90) REVERT: C 29 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7596 (tpp80) REVERT: C 32 ARG cc_start: 0.7979 (ttp80) cc_final: 0.6967 (ttp-110) REVERT: C 35 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8253 (tmm160) REVERT: C 75 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8338 (mmmm) REVERT: C 89 ASN cc_start: 0.8688 (m-40) cc_final: 0.8353 (m110) REVERT: C 110 ASN cc_start: 0.9064 (t0) cc_final: 0.8707 (t0) REVERT: C 115 LEU cc_start: 0.8959 (mp) cc_final: 0.8296 (mp) REVERT: D 34 TYR cc_start: 0.8398 (m-10) cc_final: 0.8148 (m-10) REVERT: D 59 MET cc_start: 0.9695 (mmm) cc_final: 0.9279 (tpp) REVERT: D 65 ASP cc_start: 0.8969 (t70) cc_final: 0.8649 (t70) REVERT: D 69 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8430 (mtp180) REVERT: D 92 GLN cc_start: 0.8243 (pt0) cc_final: 0.7768 (pp30) REVERT: D 102 GLU cc_start: 0.8006 (tp30) cc_final: 0.7692 (tp30) REVERT: D 109 SER cc_start: 0.9149 (t) cc_final: 0.8621 (p) REVERT: D 110 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8085 (mt-10) REVERT: D 113 LYS cc_start: 0.9235 (mtmm) cc_final: 0.9016 (mmtm) REVERT: F 63 GLU cc_start: 0.7633 (pp20) cc_final: 0.6878 (pp20) REVERT: F 78 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8472 (tpp80) REVERT: F 88 TYR cc_start: 0.9311 (m-10) cc_final: 0.8848 (m-80) REVERT: G 24 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7192 (mp10) REVERT: G 39 TYR cc_start: 0.8990 (m-80) cc_final: 0.8728 (m-80) REVERT: G 42 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8166 (mtm-85) REVERT: G 61 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 64 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7698 (tm-30) REVERT: G 68 ASN cc_start: 0.8555 (p0) cc_final: 0.7911 (p0) REVERT: G 72 ASP cc_start: 0.7861 (m-30) cc_final: 0.7560 (m-30) REVERT: G 78 ILE cc_start: 0.8845 (mt) cc_final: 0.8581 (mt) REVERT: G 81 ARG cc_start: 0.8751 (tpt90) cc_final: 0.8504 (tpt90) REVERT: G 84 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8776 (tp-100) REVERT: G 85 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8736 (mt) REVERT: G 89 ASN cc_start: 0.8578 (p0) cc_final: 0.8302 (p0) REVERT: G 95 LYS cc_start: 0.9213 (pttp) cc_final: 0.8602 (ptpp) REVERT: G 116 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8032 (mt) REVERT: H 40 LYS cc_start: 0.9392 (tppt) cc_final: 0.8863 (tppt) REVERT: H 56 MET cc_start: 0.8020 (tmm) cc_final: 0.7721 (tmm) REVERT: H 73 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8570 (mm-30) REVERT: H 76 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8486 (mtm110) REVERT: H 102 GLU cc_start: 0.8989 (mm-30) cc_final: 0.7934 (mm-30) REVERT: H 110 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8557 (tt0) REVERT: H 113 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8980 (ptpt) REVERT: K 40 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4573 (tp) REVERT: K 79 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6209 (pt0) REVERT: A 49 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8265 (mtm110) REVERT: A 76 GLN cc_start: 0.8856 (mm110) cc_final: 0.8477 (mm-40) REVERT: A 93 GLN cc_start: 0.7971 (tt0) cc_final: 0.7681 (mt0) REVERT: A 106 ASP cc_start: 0.8531 (m-30) cc_final: 0.8192 (m-30) REVERT: E 39 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6823 (p-80) REVERT: E 56 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7863 (mmtm) REVERT: E 60 LEU cc_start: 0.8743 (mm) cc_final: 0.8450 (tt) REVERT: E 73 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: E 85 GLN cc_start: 0.8097 (mt0) cc_final: 0.7391 (mt0) REVERT: E 105 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7586 (tm-30) REVERT: E 108 ASN cc_start: 0.9418 (t0) cc_final: 0.9184 (t0) REVERT: E 115 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8527 (mmmm) REVERT: E 117 VAL cc_start: 0.9379 (t) cc_final: 0.9167 (p) REVERT: E 118 THR cc_start: 0.9086 (m) cc_final: 0.8494 (p) REVERT: E 120 MET cc_start: 0.6817 (mtp) cc_final: 0.6273 (mpp) outliers start: 48 outliers final: 36 residues processed: 402 average time/residue: 0.1379 time to fit residues: 73.4289 Evaluate side-chains 415 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 373 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 64 ASN G 73 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.139402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094803 restraints weight = 29332.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097942 restraints weight = 16102.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100027 restraints weight = 11144.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101255 restraints weight = 8855.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102026 restraints weight = 7746.536| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13814 Z= 0.178 Angle : 0.728 10.817 19943 Z= 0.407 Chirality : 0.045 0.265 2253 Planarity : 0.006 0.062 1485 Dihedral : 30.205 158.604 4239 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 7.29 % Allowed : 35.62 % Favored : 57.08 % 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: 0.08 (0.28), residues: 831 helix: 0.61 (0.22), residues: 530 sheet: -3.38 (1.44), residues: 10 loop : -0.70 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.019 0.002 TYR G 57 PHE 0.028 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (13814) covalent geometry : angle 0.72799 / 0.41 (19943) hydrogen bonds : bond 0.05923 / 3.76 ( 658) hydrogen bonds : angle 3.36259 / 2.26 ( 1637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 385 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9372 (mtp85) cc_final: 0.8988 (mtp85) REVERT: B 45 ARG cc_start: 0.9135 (mtp-110) cc_final: 0.8781 (mtp85) REVERT: B 53 GLU cc_start: 0.8513 (tp30) cc_final: 0.8135 (tp30) REVERT: B 61 PHE cc_start: 0.8971 (t80) cc_final: 0.8701 (t80) REVERT: B 63 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7777 (mt-10) REVERT: B 73 THR cc_start: 0.9341 (t) cc_final: 0.9140 (t) REVERT: C 17 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8571 (mtt90) REVERT: C 20 ARG cc_start: 0.8814 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: C 29 ARG cc_start: 0.8376 (tpp80) cc_final: 0.6478 (tpp80) REVERT: C 32 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7027 (ttp-170) REVERT: C 75 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8446 (mmmm) REVERT: C 89 ASN cc_start: 0.8786 (m-40) cc_final: 0.8445 (m110) REVERT: C 110 ASN cc_start: 0.9024 (t0) cc_final: 0.8707 (t0) REVERT: D 39 TYR cc_start: 0.8353 (t80) cc_final: 0.7716 (t80) REVERT: D 43 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8566 (tppt) REVERT: D 65 ASP cc_start: 0.9011 (t70) cc_final: 0.8706 (t70) REVERT: D 69 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.8591 (mtp180) REVERT: D 83 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: D 92 GLN cc_start: 0.8407 (pt0) cc_final: 0.7784 (pp30) REVERT: D 102 GLU cc_start: 0.8004 (tp30) cc_final: 0.7685 (tp30) REVERT: D 109 SER cc_start: 0.9271 (t) cc_final: 0.8670 (p) REVERT: D 113 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8953 (mmtm) REVERT: F 63 GLU cc_start: 0.7585 (pp20) cc_final: 0.6840 (pp20) REVERT: F 78 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8535 (tpp80) REVERT: F 88 TYR cc_start: 0.9243 (m-10) cc_final: 0.8704 (m-80) REVERT: F 90 LEU cc_start: 0.9293 (mt) cc_final: 0.9019 (mp) REVERT: G 42 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8169 (mtm-85) REVERT: G 61 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8097 (mm-30) REVERT: G 64 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7787 (tm-30) REVERT: G 68 ASN cc_start: 0.8569 (p0) cc_final: 0.7912 (p0) REVERT: G 78 ILE cc_start: 0.8835 (mt) cc_final: 0.8593 (mt) REVERT: G 81 ARG cc_start: 0.8837 (tpt90) cc_final: 0.8604 (tpt90) REVERT: G 89 ASN cc_start: 0.8601 (p0) cc_final: 0.8320 (p0) REVERT: G 95 LYS cc_start: 0.9217 (pttp) cc_final: 0.8598 (ptpp) REVERT: G 116 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8038 (mt) REVERT: H 39 TYR cc_start: 0.8505 (t80) cc_final: 0.8300 (t80) REVERT: H 40 LYS cc_start: 0.9375 (tppt) cc_final: 0.8759 (tppt) REVERT: H 43 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8184 (pptt) REVERT: H 44 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7353 (mm110) REVERT: H 56 MET cc_start: 0.8111 (tmm) cc_final: 0.7788 (tmm) REVERT: H 102 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8815 (mm-30) REVERT: H 113 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8995 (ptpt) REVERT: K 79 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6220 (pt0) REVERT: A 49 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8409 (mtm-85) REVERT: A 53 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.7338 (tmm-80) REVERT: A 56 LYS cc_start: 0.8497 (pttp) cc_final: 0.8203 (pttm) REVERT: A 76 GLN cc_start: 0.8898 (mm110) cc_final: 0.8485 (mm-40) REVERT: A 106 ASP cc_start: 0.8530 (m-30) cc_final: 0.8224 (m-30) REVERT: E 39 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6915 (p-80) REVERT: E 56 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7844 (mptt) REVERT: E 57 SER cc_start: 0.8588 (m) cc_final: 0.8169 (m) REVERT: E 60 LEU cc_start: 0.9055 (mm) cc_final: 0.7954 (mm) REVERT: E 76 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8690 (tm-30) REVERT: E 85 GLN cc_start: 0.8168 (mt0) cc_final: 0.7872 (mt0) REVERT: E 93 GLN cc_start: 0.8695 (tt0) cc_final: 0.8413 (tm-30) REVERT: E 105 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 108 ASN cc_start: 0.9394 (t0) cc_final: 0.9111 (t0) REVERT: E 115 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8509 (mmmm) REVERT: E 118 THR cc_start: 0.9031 (m) cc_final: 0.8558 (p) REVERT: E 119 ILE cc_start: 0.8901 (pt) cc_final: 0.7976 (pt) REVERT: E 120 MET cc_start: 0.7042 (mtp) cc_final: 0.6488 (mpp) REVERT: E 125 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8122 (mp10) outliers start: 52 outliers final: 41 residues processed: 397 average time/residue: 0.1405 time to fit residues: 74.0979 Evaluate side-chains 420 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 375 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 73 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095418 restraints weight = 29704.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098597 restraints weight = 16184.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100605 restraints weight = 11118.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.101898 restraints weight = 8870.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102670 restraints weight = 7739.297| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13814 Z= 0.167 Angle : 0.740 11.691 19943 Z= 0.412 Chirality : 0.045 0.265 2253 Planarity : 0.006 0.063 1485 Dihedral : 30.189 158.266 4237 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.47 % Allowed : 38.43 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 831 helix: 0.74 (0.22), residues: 528 sheet: -3.29 (1.47), residues: 10 loop : -0.75 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 35 TYR 0.046 0.002 TYR C 57 PHE 0.026 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (13814) covalent geometry : angle 0.73968 / 0.41 (19943) hydrogen bonds : bond 0.05754 / 3.64 ( 658) hydrogen bonds : angle 3.37030 / 2.25 ( 1637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 382 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8999 (tppt) REVERT: B 44 LYS cc_start: 0.9314 (mttt) cc_final: 0.8701 (mttp) REVERT: B 45 ARG cc_start: 0.9166 (mtp-110) cc_final: 0.8796 (mtp85) REVERT: B 53 GLU cc_start: 0.8478 (tp30) cc_final: 0.8088 (tp30) REVERT: B 63 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 17 ARG cc_start: 0.8896 (mtm180) cc_final: 0.8563 (mtt90) REVERT: C 20 ARG cc_start: 0.8772 (mmt-90) cc_final: 0.8429 (mmt-90) REVERT: C 24 GLN cc_start: 0.8775 (mm-40) cc_final: 0.7754 (mm-40) REVERT: C 25 PHE cc_start: 0.9011 (m-10) cc_final: 0.8718 (m-10) REVERT: C 29 ARG cc_start: 0.8339 (tpp80) cc_final: 0.6385 (tpp80) REVERT: C 32 ARG cc_start: 0.8004 (ttp80) cc_final: 0.6878 (ttp-170) REVERT: C 35 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8229 (ttp80) REVERT: C 36 LYS cc_start: 0.8139 (pttm) cc_final: 0.7864 (mtmm) REVERT: C 75 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8453 (mmmm) REVERT: C 89 ASN cc_start: 0.8762 (m-40) cc_final: 0.8452 (m110) REVERT: C 110 ASN cc_start: 0.9043 (t0) cc_final: 0.8728 (t0) REVERT: C 115 LEU cc_start: 0.8593 (mp) cc_final: 0.8292 (mp) REVERT: C 116 LEU cc_start: 0.8822 (tp) cc_final: 0.8588 (mt) REVERT: D 39 TYR cc_start: 0.8269 (t80) cc_final: 0.7680 (t80) REVERT: D 43 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8758 (tppt) REVERT: D 65 ASP cc_start: 0.9019 (t70) cc_final: 0.8685 (t70) REVERT: D 69 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8607 (mtp180) REVERT: D 83 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7522 (mmm-85) REVERT: D 92 GLN cc_start: 0.8396 (pt0) cc_final: 0.7753 (pp30) REVERT: D 102 GLU cc_start: 0.7892 (tp30) cc_final: 0.7643 (tp30) REVERT: D 109 SER cc_start: 0.9259 (t) cc_final: 0.8655 (p) REVERT: D 110 GLU cc_start: 0.8907 (tt0) cc_final: 0.8481 (mt-10) REVERT: D 113 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8927 (mmtm) REVERT: F 63 GLU cc_start: 0.7565 (pp20) cc_final: 0.6663 (pp20) REVERT: F 78 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8596 (tpp80) REVERT: F 88 TYR cc_start: 0.9255 (m-10) cc_final: 0.8836 (m-80) REVERT: F 90 LEU cc_start: 0.9288 (mt) cc_final: 0.9012 (mp) REVERT: G 17 ARG cc_start: 0.8529 (mtm180) cc_final: 0.7767 (mtt90) REVERT: G 42 ARG cc_start: 0.8715 (mtp-110) cc_final: 0.8228 (mtm-85) REVERT: G 61 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 64 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 68 ASN cc_start: 0.8560 (p0) cc_final: 0.7940 (p0) REVERT: G 78 ILE cc_start: 0.8841 (mt) cc_final: 0.8587 (mt) REVERT: G 81 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8568 (tpt90) REVERT: G 89 ASN cc_start: 0.8558 (p0) cc_final: 0.8300 (p0) REVERT: G 95 LYS cc_start: 0.9216 (pttp) cc_final: 0.8763 (ptpp) REVERT: G 116 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8050 (mt) REVERT: H 39 TYR cc_start: 0.8364 (t80) cc_final: 0.8154 (t80) REVERT: H 40 LYS cc_start: 0.9342 (tppt) cc_final: 0.8827 (tppt) REVERT: H 43 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8137 (pptt) REVERT: H 48 ASP cc_start: 0.8778 (m-30) cc_final: 0.8223 (p0) REVERT: H 56 MET cc_start: 0.8127 (tmm) cc_final: 0.7807 (tmm) REVERT: H 76 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8649 (mtm110) REVERT: H 113 LYS cc_start: 0.9306 (mtmt) cc_final: 0.9005 (ptpt) REVERT: H 117 LYS cc_start: 0.8858 (tppt) cc_final: 0.8436 (tmmt) REVERT: K 79 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6238 (pt0) REVERT: A 76 GLN cc_start: 0.8871 (mm110) cc_final: 0.8475 (mm-40) REVERT: A 106 ASP cc_start: 0.8475 (m-30) cc_final: 0.8114 (m-30) REVERT: E 39 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6953 (p-80) REVERT: E 57 SER cc_start: 0.8736 (m) cc_final: 0.8512 (m) REVERT: E 60 LEU cc_start: 0.8966 (mm) cc_final: 0.7447 (mm) REVERT: E 76 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8487 (tm-30) REVERT: E 85 GLN cc_start: 0.8178 (mt0) cc_final: 0.7818 (mt0) REVERT: E 93 GLN cc_start: 0.8729 (tt0) cc_final: 0.8389 (tm-30) REVERT: E 97 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8570 (mt-10) REVERT: E 105 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 108 ASN cc_start: 0.9334 (t0) cc_final: 0.9083 (t0) REVERT: E 115 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8432 (mmmm) REVERT: E 119 ILE cc_start: 0.8948 (pt) cc_final: 0.8048 (pt) REVERT: E 120 MET cc_start: 0.7030 (mtp) cc_final: 0.6520 (mpp) outliers start: 39 outliers final: 30 residues processed: 392 average time/residue: 0.1322 time to fit residues: 69.1398 Evaluate side-chains 406 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 88 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 0.0970 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 73 ASN K 78 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.139652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094654 restraints weight = 29982.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097827 restraints weight = 16584.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099871 restraints weight = 11479.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101165 restraints weight = 9173.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101947 restraints weight = 7994.652| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13814 Z= 0.169 Angle : 0.760 13.938 19943 Z= 0.420 Chirality : 0.045 0.257 2253 Planarity : 0.006 0.066 1485 Dihedral : 30.198 158.186 4237 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.05 % Allowed : 38.43 % Favored : 56.52 % 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: 0.20 (0.28), residues: 831 helix: 0.74 (0.22), residues: 528 sheet: -3.29 (1.50), residues: 10 loop : -0.74 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 92 TYR 0.028 0.002 TYR H 37 PHE 0.029 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (13814) covalent geometry : angle 0.75991 / 0.42 (19943) hydrogen bonds : bond 0.05702 / 3.62 ( 658) hydrogen bonds : angle 3.35867 / 2.25 ( 1637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.9338 (ttmm) cc_final: 0.8996 (tptp) REVERT: B 35 ARG cc_start: 0.9074 (mtp85) cc_final: 0.8772 (ttm110) REVERT: B 44 LYS cc_start: 0.9316 (mttt) cc_final: 0.8931 (mttt) REVERT: B 45 ARG cc_start: 0.9100 (mtp-110) cc_final: 0.8704 (mtp85) REVERT: B 53 GLU cc_start: 0.8494 (tp30) cc_final: 0.8095 (tp30) REVERT: C 17 ARG cc_start: 0.8911 (mtm180) cc_final: 0.8596 (mtt90) REVERT: C 20 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8520 (mmt-90) REVERT: C 24 GLN cc_start: 0.8600 (mm-40) cc_final: 0.7356 (mm-40) REVERT: C 25 PHE cc_start: 0.9088 (m-10) cc_final: 0.8812 (m-10) REVERT: C 29 ARG cc_start: 0.8349 (tpp80) cc_final: 0.6374 (tpp80) REVERT: C 32 ARG cc_start: 0.8021 (ttp80) cc_final: 0.6867 (ttp-170) REVERT: C 35 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7946 (ttp80) REVERT: C 36 LYS cc_start: 0.8251 (pttm) cc_final: 0.8031 (mtmm) REVERT: C 75 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8464 (mmmm) REVERT: C 84 GLN cc_start: 0.9310 (tp40) cc_final: 0.9077 (tp-100) REVERT: C 89 ASN cc_start: 0.8728 (m-40) cc_final: 0.8393 (m110) REVERT: C 110 ASN cc_start: 0.9086 (t0) cc_final: 0.8804 (t0) REVERT: D 39 TYR cc_start: 0.8268 (t80) cc_final: 0.7702 (t80) REVERT: D 43 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8814 (tppt) REVERT: D 65 ASP cc_start: 0.8990 (t70) cc_final: 0.8688 (t70) REVERT: D 69 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8541 (mtp180) REVERT: D 83 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7353 (mmt180) REVERT: D 92 GLN cc_start: 0.8324 (pt0) cc_final: 0.7862 (pp30) REVERT: D 102 GLU cc_start: 0.7874 (tp30) cc_final: 0.7613 (tp30) REVERT: D 109 SER cc_start: 0.9350 (t) cc_final: 0.8641 (p) REVERT: D 113 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8903 (mmtm) REVERT: F 63 GLU cc_start: 0.7604 (pp20) cc_final: 0.6709 (pp20) REVERT: F 78 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8560 (tpp80) REVERT: F 88 TYR cc_start: 0.9186 (m-10) cc_final: 0.8668 (m-80) REVERT: F 90 LEU cc_start: 0.9316 (mt) cc_final: 0.9055 (mp) REVERT: G 20 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8133 (mtm180) REVERT: G 35 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7669 (mmp80) REVERT: G 42 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8191 (mtm-85) REVERT: G 61 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8111 (mm-30) REVERT: G 64 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7763 (tm-30) REVERT: G 68 ASN cc_start: 0.8543 (p0) cc_final: 0.7887 (p0) REVERT: G 78 ILE cc_start: 0.8953 (mt) cc_final: 0.8678 (mt) REVERT: G 79 ILE cc_start: 0.8651 (mm) cc_final: 0.8429 (mm) REVERT: G 81 ARG cc_start: 0.8947 (tpt90) cc_final: 0.8516 (tpt90) REVERT: G 89 ASN cc_start: 0.8498 (p0) cc_final: 0.8286 (p0) REVERT: G 116 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8040 (mt) REVERT: H 40 LYS cc_start: 0.9350 (tppt) cc_final: 0.8824 (tppt) REVERT: H 43 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8221 (pptt) REVERT: H 48 ASP cc_start: 0.8773 (m-30) cc_final: 0.8253 (p0) REVERT: H 56 MET cc_start: 0.8144 (tmm) cc_final: 0.7823 (tmm) REVERT: H 113 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8998 (ptpt) REVERT: K 79 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6248 (pt0) REVERT: A 49 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8216 (mtm110) REVERT: A 76 GLN cc_start: 0.8895 (mm110) cc_final: 0.8525 (mm-40) REVERT: A 106 ASP cc_start: 0.8422 (m-30) cc_final: 0.7962 (m-30) REVERT: E 39 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.7209 (p-80) REVERT: E 57 SER cc_start: 0.8839 (m) cc_final: 0.8636 (m) REVERT: E 60 LEU cc_start: 0.8946 (mm) cc_final: 0.7900 (mm) REVERT: E 76 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8524 (tm-30) REVERT: E 85 GLN cc_start: 0.8536 (mt0) cc_final: 0.8069 (mt0) REVERT: E 93 GLN cc_start: 0.8822 (tt0) cc_final: 0.8519 (tm-30) REVERT: E 97 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 105 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 115 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8481 (mmmm) REVERT: E 119 ILE cc_start: 0.8919 (pt) cc_final: 0.8076 (pt) REVERT: E 120 MET cc_start: 0.7105 (mtp) cc_final: 0.6586 (mpp) outliers start: 36 outliers final: 27 residues processed: 391 average time/residue: 0.1276 time to fit residues: 66.4726 Evaluate side-chains 405 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 374 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 93 optimal weight: 0.0370 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095661 restraints weight = 29767.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098792 restraints weight = 16450.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100869 restraints weight = 11392.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102152 restraints weight = 9066.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102917 restraints weight = 7922.005| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13814 Z= 0.162 Angle : 0.747 18.109 19943 Z= 0.412 Chirality : 0.045 0.255 2253 Planarity : 0.006 0.064 1485 Dihedral : 30.190 158.059 4237 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.07 % Allowed : 39.97 % Favored : 55.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 831 helix: 0.71 (0.22), residues: 528 sheet: -3.26 (1.49), residues: 10 loop : -0.68 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 76 TYR 0.032 0.002 TYR G 39 PHE 0.029 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (13814) covalent geometry : angle 0.74740 / 0.41 (19943) hydrogen bonds : bond 0.05601 / 3.55 ( 658) hydrogen bonds : angle 3.37558 / 2.23 ( 1637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.72 seconds wall clock time: 43 minutes 39.09 seconds (2619.09 seconds total)