Starting phenix.real_space_refine on Thu Aug 6 00:50:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbq_16549/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cbq_16549/08_2026/8cbq_16549.cif" } 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-2.2rc3-6140/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: 2.31, per 1000 atoms: 0.18 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: 1.02 Conformation dependent library (CDL) restraints added in 421.3 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: 1.88 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: 1.92 Time building geometry restraints manager: 1.43 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: 18384 1.60 - 3.20: 1484 3.20 - 4.79: 54 4.79 - 6.39: 14 6.39 - 7.99: 7 Bond angle restraints: 19943 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 119.70 125.91 -6.21 1.20e+00 6.94e-01 2.68e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.62 -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=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 119.70 125.03 -5.33 1.20e+00 6.94e-01 1.97e+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 ... (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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.130 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- 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= 0.721 Angle : 0.856 7.992 19943 Z= 0.705 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 0.85626 / 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 : 0.286 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: 0.7407 (mt) REVERT: B 44 LYS cc_start: 0.8631 (tttt) cc_final: 0.8379 (mtmt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7391 (tp30) REVERT: C 32 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6622 (ttp-170) REVERT: C 62 ILE cc_start: 0.9381 (mt) cc_final: 0.9075 (mm) REVERT: C 68 ASN cc_start: 0.8832 (m-40) cc_final: 0.8228 (m-40) REVERT: C 83 LEU cc_start: 0.9336 (mt) cc_final: 0.8973 (mt) REVERT: C 87 VAL cc_start: 0.9403 (m) cc_final: 0.9120 (m) REVERT: C 110 ASN cc_start: 0.7942 (t0) cc_final: 0.7372 (t0) REVERT: D 49 THR cc_start: 0.8903 (m) cc_final: 0.8699 (m) REVERT: D 59 MET cc_start: 0.8965 (mmm) cc_final: 0.8378 (tpp) REVERT: D 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7289 (mt-10) REVERT: F 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.7836 (m110) REVERT: F 34 ILE cc_start: 0.8857 (mt) cc_final: 0.8628 (mm) REVERT: F 39 ARG cc_start: 0.9036 (mmt-90) cc_final: 0.8787 (mmt180) REVERT: F 88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8436 (m-80) REVERT: G 20 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7424 (mtt90) REVERT: G 57 TYR cc_start: 0.8128 (t80) cc_final: 0.7799 (t80) REVERT: G 110 ASN cc_start: 0.8643 (t0) cc_final: 0.8248 (t0) REVERT: H 84 SER cc_start: 0.8697 (m) cc_final: 0.8423 (p) REVERT: H 110 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8296 (mt-10) REVERT: H 113 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8239 (tppt) REVERT: K 40 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2397 (tp) REVERT: A 46 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8797 (t) 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: 0.7889 (mt0) REVERT: A 62 ILE cc_start: 0.8573 (mt) cc_final: 0.8235 (mt) REVERT: A 76 GLN cc_start: 0.8258 (mm110) cc_final: 0.7919 (mm-40) REVERT: A 84 PHE cc_start: 0.8420 (m-80) cc_final: 0.7651 (m-80) REVERT: A 99 TYR cc_start: 0.8300 (t80) cc_final: 0.8095 (t80) REVERT: A 120 MET cc_start: 0.7237 (mtp) cc_final: 0.6925 (mmm) REVERT: E 60 LEU cc_start: 0.8200 (mt) cc_final: 0.7428 (mp) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9190 (t) REVERT: E 74 ILE cc_start: 0.9177 (mt) cc_final: 0.8900 (tt) REVERT: E 118 THR cc_start: 0.8515 (m) cc_final: 0.7593 (p) REVERT: E 119 ILE cc_start: 0.8810 (pt) cc_final: 0.7802 (pt) REVERT: E 120 MET cc_start: 0.7605 (mtt) cc_final: 0.6550 (mpp) outliers start: 13 outliers final: 6 residues processed: 468 average time/residue: 0.1750 time to fit residues: 106.4639 Evaluate side-chains 375 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 367 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 H 106 HIS K 64 ASN K 86 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107565 restraints weight = 28783.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.111223 restraints weight = 14949.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113566 restraints weight = 9909.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115065 restraints weight = 7676.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115997 restraints weight = 6581.725| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 13814 Z= 0.204 Angle : 0.851 7.955 19943 Z= 0.472 Chirality : 0.053 0.273 2253 Planarity : 0.008 0.089 1485 Dihedral : 29.844 168.133 4250 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.91 % Allowed : 24.40 % Favored : 70.69 % 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: -2.97 (0.23), residues: 831 helix: -1.96 (0.18), residues: 523 sheet: -3.94 (1.04), residues: 17 loop : -1.47 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 89 TYR 0.029 0.003 TYR F 51 PHE 0.024 0.003 PHE A 78 TRP 0.002 0.001 TRP K 82 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (13814) covalent geometry : angle 0.85109 / 0.47 (19943) hydrogen bonds : bond 0.08594 / 5.53 ( 658) hydrogen bonds : angle 3.85428 / 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 431 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 396 time to evaluate : 0.364 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: B 25 ASN cc_start: 0.8851 (m110) cc_final: 0.8412 (m-40) REVERT: B 53 GLU cc_start: 0.8338 (tp30) cc_final: 0.7987 (tp30) REVERT: B 64 ASN cc_start: 0.8831 (m-40) cc_final: 0.8574 (t0) REVERT: B 79 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8301 (mmtm) REVERT: C 32 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7406 (tmm-80) REVERT: C 36 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7173 (mtmm) REVERT: C 42 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: C 56 GLU cc_start: 0.8668 (tt0) cc_final: 0.7832 (tt0) REVERT: C 71 ARG cc_start: 0.7566 (ttm110) cc_final: 0.7170 (ttp-110) REVERT: C 73 ASN cc_start: 0.8764 (m-40) cc_final: 0.8391 (m-40) REVERT: C 75 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8278 (mmmm) REVERT: C 95 LYS cc_start: 0.9028 (ptpt) cc_final: 0.8723 (pttt) REVERT: C 110 ASN cc_start: 0.8751 (t0) cc_final: 0.8248 (t0) REVERT: D 34 TYR cc_start: 0.8731 (m-80) cc_final: 0.8365 (m-80) REVERT: D 65 ASP cc_start: 0.8630 (t70) cc_final: 0.8229 (t70) REVERT: D 105 LYS cc_start: 0.8539 (tptp) cc_final: 0.8336 (tptp) REVERT: D 110 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7637 (mt-10) REVERT: D 113 LYS cc_start: 0.9196 (mmtm) cc_final: 0.8822 (mmtm) REVERT: D 117 LYS cc_start: 0.9353 (tttt) cc_final: 0.9114 (pttp) REVERT: F 25 ASN cc_start: 0.8652 (m-40) cc_final: 0.7971 (m-40) REVERT: F 39 ARG cc_start: 0.9205 (mmt-90) cc_final: 0.8908 (mmt180) REVERT: F 53 GLU cc_start: 0.8619 (tp30) cc_final: 0.8215 (tp30) REVERT: F 88 TYR cc_start: 0.9271 (m-10) cc_final: 0.8766 (m-80) REVERT: G 17 ARG cc_start: 0.8407 (mtm180) cc_final: 0.7694 (ptp-170) REVERT: G 29 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.6024 (tpp80) REVERT: G 61 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8253 (mm-30) REVERT: G 68 ASN cc_start: 0.8529 (p0) cc_final: 0.8190 (p0) REVERT: G 73 ASN cc_start: 0.8907 (t0) cc_final: 0.8507 (t0) REVERT: G 81 ARG cc_start: 0.8329 (tpt90) cc_final: 0.8060 (tpt90) REVERT: G 92 GLU cc_start: 0.8607 (pm20) cc_final: 0.8135 (pm20) REVERT: G 110 ASN cc_start: 0.8844 (t0) cc_final: 0.8342 (t0) REVERT: H 31 LYS cc_start: 0.9086 (mppt) cc_final: 0.8779 (mppt) REVERT: H 40 LYS cc_start: 0.8979 (tppt) cc_final: 0.8467 (tppt) REVERT: H 43 LYS cc_start: 0.8625 (pptt) cc_final: 0.7841 (pptt) REVERT: H 44 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8117 (mm-40) REVERT: H 49 THR cc_start: 0.9022 (p) cc_final: 0.8774 (p) REVERT: H 73 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8669 (mm-30) REVERT: H 84 SER cc_start: 0.8567 (m) cc_final: 0.8200 (p) REVERT: H 102 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8360 (mm-30) REVERT: H 110 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8243 (tt0) REVERT: H 113 LYS cc_start: 0.9331 (mtmt) cc_final: 0.8934 (ptpt) REVERT: K 40 LEU cc_start: 0.3416 (OUTLIER) cc_final: 0.3046 (tp) REVERT: A 55 GLN cc_start: 0.9063 (mt0) cc_final: 0.8568 (tt0) REVERT: A 56 LYS cc_start: 0.8453 (pttp) cc_final: 0.8151 (ptpp) REVERT: A 73 GLU cc_start: 0.6848 (tp30) cc_final: 0.6125 (tp30) REVERT: A 76 GLN cc_start: 0.8664 (mm110) cc_final: 0.8197 (mm-40) REVERT: A 79 LYS cc_start: 0.8696 (tptp) cc_final: 0.8085 (tptp) REVERT: A 84 PHE cc_start: 0.8418 (m-80) cc_final: 0.7549 (m-80) REVERT: A 106 ASP cc_start: 0.8668 (m-30) cc_final: 0.8378 (m-30) REVERT: A 129 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8131 (mmp80) REVERT: E 49 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8140 (ptp-170) REVERT: E 54 TYR cc_start: 0.7880 (m-10) cc_final: 0.7595 (m-10) REVERT: E 60 LEU cc_start: 0.9113 (mt) cc_final: 0.8756 (mm) REVERT: E 67 PHE cc_start: 0.8566 (t80) cc_final: 0.7725 (t80) REVERT: E 71 VAL cc_start: 0.9144 (t) cc_final: 0.8849 (t) REVERT: E 78 PHE cc_start: 0.8190 (m-10) cc_final: 0.7978 (m-80) REVERT: E 85 GLN cc_start: 0.8033 (mt0) cc_final: 0.7531 (mt0) REVERT: E 93 GLN cc_start: 0.8676 (tm-30) cc_final: 0.7741 (tm-30) REVERT: E 105 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7418 (tm-30) REVERT: E 117 VAL cc_start: 0.8908 (t) cc_final: 0.8649 (p) REVERT: E 119 ILE cc_start: 0.9059 (pt) cc_final: 0.8092 (pt) REVERT: E 120 MET cc_start: 0.6705 (mtt) cc_final: 0.6359 (mpp) REVERT: E 125 GLN cc_start: 0.8711 (mt0) cc_final: 0.8426 (mm-40) outliers start: 35 outliers final: 24 residues processed: 408 average time/residue: 0.1557 time to fit residues: 84.3467 Evaluate side-chains 399 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 372 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR 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 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 33 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 93 THR 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 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL 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: 0.0010 chunk 108 optimal weight: 0.9990 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: 0.1980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN H 46 HIS H 92 GLN A 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.147001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103940 restraints weight = 29017.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107466 restraints weight = 15125.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109712 restraints weight = 10123.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111153 restraints weight = 7882.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.111980 restraints weight = 6792.593| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 13814 Z= 0.168 Angle : 0.770 10.128 19943 Z= 0.431 Chirality : 0.049 0.278 2253 Planarity : 0.006 0.071 1485 Dihedral : 30.112 163.397 4249 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.19 % Allowed : 28.47 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.27), residues: 831 helix: -0.51 (0.22), residues: 521 sheet: -4.12 (1.35), residues: 10 loop : -1.05 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 129 TYR 0.026 0.002 TYR F 51 PHE 0.014 0.002 PHE F 61 TRP 0.004 0.001 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (13814) covalent geometry : angle 0.77016 / 0.43 (19943) hydrogen bonds : bond 0.07040 / 4.50 ( 658) hydrogen bonds : angle 3.51344 / 2.37 ( 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 428 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 391 time to evaluate : 0.326 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 25 ASN cc_start: 0.8625 (m110) cc_final: 0.8421 (m110) REVERT: B 45 ARG cc_start: 0.8492 (mtp-110) cc_final: 0.8273 (ttp80) REVERT: B 53 GLU cc_start: 0.8431 (tp30) cc_final: 0.8157 (tp30) REVERT: B 63 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 42 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7917 (mtm-85) REVERT: C 56 GLU cc_start: 0.8572 (tt0) cc_final: 0.8369 (tt0) REVERT: C 71 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7338 (ttp-110) REVERT: C 95 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8815 (pttt) REVERT: C 110 ASN cc_start: 0.8832 (t0) cc_final: 0.8371 (t0) REVERT: C 115 LEU cc_start: 0.9090 (mp) cc_final: 0.8710 (mp) REVERT: D 59 MET cc_start: 0.9565 (mmm) cc_final: 0.8971 (tpp) REVERT: D 64 ASN cc_start: 0.8258 (m110) cc_final: 0.7893 (m110) REVERT: D 65 ASP cc_start: 0.8858 (t70) cc_final: 0.8414 (t70) REVERT: D 102 GLU cc_start: 0.7903 (tp30) cc_final: 0.7688 (tp30) REVERT: D 110 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7682 (mt-10) REVERT: D 113 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8838 (mmtm) REVERT: D 117 LYS cc_start: 0.9346 (tttt) cc_final: 0.8992 (ttpp) REVERT: F 25 ASN cc_start: 0.8601 (m-40) cc_final: 0.8137 (m-40) REVERT: F 39 ARG cc_start: 0.9149 (mmt-90) cc_final: 0.8861 (mmt180) REVERT: F 51 TYR cc_start: 0.7773 (m-80) cc_final: 0.7448 (m-10) REVERT: F 53 GLU cc_start: 0.8597 (tp30) cc_final: 0.8144 (tp30) REVERT: F 61 PHE cc_start: 0.8740 (t80) cc_final: 0.8501 (t80) REVERT: F 88 TYR cc_start: 0.9243 (m-10) cc_final: 0.8743 (m-80) REVERT: G 17 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7486 (ptp-170) REVERT: G 32 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8242 (ttp80) REVERT: G 61 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8059 (mm-30) REVERT: G 68 ASN cc_start: 0.8353 (p0) cc_final: 0.7975 (p0) REVERT: G 73 ASN cc_start: 0.8456 (t0) cc_final: 0.8217 (t0) REVERT: G 81 ARG cc_start: 0.8467 (tpt90) cc_final: 0.8157 (tpt90) REVERT: G 95 LYS cc_start: 0.9024 (pttp) cc_final: 0.8798 (pttp) REVERT: G 110 ASN cc_start: 0.8911 (t0) cc_final: 0.8370 (t0) REVERT: H 39 TYR cc_start: 0.8292 (t80) cc_final: 0.7989 (t80) REVERT: H 40 LYS cc_start: 0.9486 (tppt) cc_final: 0.9146 (tppt) REVERT: H 49 THR cc_start: 0.9122 (p) cc_final: 0.8916 (p) REVERT: H 56 MET cc_start: 0.8091 (tmm) cc_final: 0.7844 (tmm) REVERT: H 59 MET cc_start: 0.8803 (mmp) cc_final: 0.8411 (mmp) REVERT: H 84 SER cc_start: 0.8562 (m) cc_final: 0.8232 (p) REVERT: H 102 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8340 (mm-30) REVERT: H 110 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8450 (tt0) REVERT: H 113 LYS cc_start: 0.9340 (mtmt) cc_final: 0.8956 (ptpt) REVERT: K 40 LEU cc_start: 0.4182 (OUTLIER) cc_final: 0.3685 (tp) REVERT: A 55 GLN cc_start: 0.9130 (mt0) cc_final: 0.8624 (tt0) REVERT: A 56 LYS cc_start: 0.8453 (pttp) cc_final: 0.8197 (ptpp) REVERT: A 73 GLU cc_start: 0.6969 (tp30) cc_final: 0.6642 (tp30) REVERT: A 76 GLN cc_start: 0.8762 (mm110) cc_final: 0.8416 (mm-40) REVERT: A 106 ASP cc_start: 0.8607 (m-30) cc_final: 0.8352 (m-30) REVERT: E 49 ARG cc_start: 0.8425 (ptm160) cc_final: 0.7783 (ptp90) REVERT: E 50 GLU cc_start: 0.8381 (pt0) cc_final: 0.8078 (pt0) REVERT: E 60 LEU cc_start: 0.9182 (mt) cc_final: 0.8981 (mm) REVERT: E 78 PHE cc_start: 0.8251 (m-10) cc_final: 0.8011 (m-80) REVERT: E 85 GLN cc_start: 0.7865 (mt0) cc_final: 0.7264 (mt0) REVERT: E 93 GLN cc_start: 0.8723 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 105 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7538 (tm-30) REVERT: E 119 ILE cc_start: 0.9040 (pt) cc_final: 0.8111 (pt) REVERT: E 120 MET cc_start: 0.6648 (mtt) cc_final: 0.6244 (mpp) REVERT: E 125 GLN cc_start: 0.8660 (mt0) cc_final: 0.8412 (mm-40) outliers start: 37 outliers final: 23 residues processed: 400 average time/residue: 0.1374 time to fit residues: 72.4116 Evaluate side-chains 399 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 375 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR 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 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 58 ILE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 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** D 64 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.144112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100370 restraints weight = 29338.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103717 restraints weight = 15595.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.105841 restraints weight = 10616.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107188 restraints weight = 8413.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107953 restraints weight = 7298.530| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13814 Z= 0.174 Angle : 0.755 7.507 19943 Z= 0.420 Chirality : 0.047 0.283 2253 Planarity : 0.006 0.061 1485 Dihedral : 30.257 160.646 4242 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.17 % Allowed : 30.43 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.27), residues: 831 helix: 0.08 (0.22), residues: 527 sheet: -3.96 (1.38), residues: 10 loop : -1.06 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 99 TYR 0.027 0.002 TYR D 37 PHE 0.014 0.002 PHE E 67 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 0.00349 / 0.17 (13814) covalent geometry : angle 0.75477 / 0.42 (19943) hydrogen bonds : bond 0.06444 / 4.13 ( 658) hydrogen bonds : angle 3.42501 / 2.32 ( 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 434 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 390 time to evaluate : 0.256 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: B 31 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8792 (tptp) REVERT: B 35 ARG cc_start: 0.9280 (mtp85) cc_final: 0.8624 (mtp85) REVERT: B 45 ARG cc_start: 0.8767 (mtp-110) cc_final: 0.8514 (ttp80) REVERT: B 53 GLU cc_start: 0.8502 (tp30) cc_final: 0.8135 (tp30) REVERT: B 63 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 17 ARG cc_start: 0.8810 (mtm180) cc_final: 0.8281 (mtt90) REVERT: C 32 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.6593 (tmm-80) REVERT: C 36 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8423 (pttp) REVERT: C 42 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7974 (mtm-85) REVERT: C 56 GLU cc_start: 0.8601 (tt0) cc_final: 0.8373 (tt0) REVERT: C 64 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8278 (tm-30) REVERT: C 71 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7427 (ttp-110) REVERT: C 75 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8482 (mmmm) REVERT: C 95 LYS cc_start: 0.9182 (ptpt) cc_final: 0.8805 (pttp) REVERT: C 110 ASN cc_start: 0.8985 (t0) cc_final: 0.8554 (t0) REVERT: C 115 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8784 (mm) REVERT: D 36 ILE cc_start: 0.9173 (pt) cc_final: 0.8968 (pt) REVERT: D 59 MET cc_start: 0.9684 (mmm) cc_final: 0.9119 (tpp) REVERT: D 64 ASN cc_start: 0.8617 (m-40) cc_final: 0.8289 (m110) REVERT: D 65 ASP cc_start: 0.8886 (t70) cc_final: 0.8536 (t70) REVERT: D 102 GLU cc_start: 0.8023 (tp30) cc_final: 0.7730 (tp30) REVERT: D 110 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7800 (mt-10) REVERT: D 113 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8746 (mmtm) REVERT: D 117 LYS cc_start: 0.9300 (tttt) cc_final: 0.8841 (ptmt) REVERT: F 25 ASN cc_start: 0.8576 (m-40) cc_final: 0.8261 (m-40) REVERT: F 31 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8238 (ttmm) REVERT: F 51 TYR cc_start: 0.7724 (m-80) cc_final: 0.7464 (m-80) REVERT: F 53 GLU cc_start: 0.8651 (tp30) cc_final: 0.8193 (tp30) REVERT: F 88 TYR cc_start: 0.9275 (m-10) cc_final: 0.8777 (m-80) REVERT: F 92 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8587 (mmm160) REVERT: G 17 ARG cc_start: 0.8252 (mtm180) cc_final: 0.7977 (ptp-170) REVERT: G 20 ARG cc_start: 0.8431 (mtt90) cc_final: 0.7987 (mtt180) REVERT: G 42 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.8278 (mtp-110) REVERT: G 61 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8246 (mm-30) REVERT: G 68 ASN cc_start: 0.8438 (p0) cc_final: 0.7996 (p0) REVERT: G 75 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8231 (mmmt) REVERT: G 78 ILE cc_start: 0.8472 (mt) cc_final: 0.8031 (mt) REVERT: G 81 ARG cc_start: 0.8598 (tpt90) cc_final: 0.8270 (tpt90) REVERT: G 95 LYS cc_start: 0.9092 (pttp) cc_final: 0.8784 (pttp) REVERT: G 110 ASN cc_start: 0.8959 (t0) cc_final: 0.8635 (t0) REVERT: H 39 TYR cc_start: 0.8318 (t80) cc_final: 0.8110 (t80) REVERT: H 40 LYS cc_start: 0.9507 (tppt) cc_final: 0.9124 (tppt) REVERT: H 56 MET cc_start: 0.8109 (tmm) cc_final: 0.7821 (tmm) REVERT: H 59 MET cc_start: 0.8942 (mmp) cc_final: 0.8570 (mmp) REVERT: H 73 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8992 (mm-30) REVERT: H 102 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8007 (mm-30) REVERT: H 110 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8500 (tt0) REVERT: H 113 LYS cc_start: 0.9338 (mtmt) cc_final: 0.8980 (ptpt) REVERT: K 40 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4322 (tp) REVERT: A 53 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8312 (tmm-80) REVERT: A 55 GLN cc_start: 0.9221 (mt0) cc_final: 0.8835 (tt0) REVERT: A 56 LYS cc_start: 0.8534 (pttp) cc_final: 0.8172 (pttp) REVERT: A 76 GLN cc_start: 0.8832 (mm110) cc_final: 0.8444 (mm-40) REVERT: A 106 ASP cc_start: 0.8519 (m-30) cc_final: 0.8165 (m-30) REVERT: E 65 LEU cc_start: 0.8921 (tp) cc_final: 0.7769 (tp) REVERT: E 74 ILE cc_start: 0.9207 (mm) cc_final: 0.8984 (tt) REVERT: E 79 LYS cc_start: 0.8005 (tppt) cc_final: 0.7793 (tppt) REVERT: E 85 GLN cc_start: 0.8041 (mt0) cc_final: 0.7460 (mt0) REVERT: E 105 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7571 (tm-30) REVERT: E 120 MET cc_start: 0.6881 (mtt) cc_final: 0.6373 (mpp) REVERT: E 125 GLN cc_start: 0.8703 (mt0) cc_final: 0.8370 (mm-40) outliers start: 44 outliers final: 28 residues processed: 406 average time/residue: 0.1232 time to fit residues: 66.5000 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 LEU 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 115 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL 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 F residue 31 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 93 THR 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 65 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 86 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 92 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN E 55 GLN E 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098605 restraints weight = 29673.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101910 restraints weight = 15931.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104045 restraints weight = 10923.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105303 restraints weight = 8673.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106152 restraints weight = 7595.668| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13814 Z= 0.169 Angle : 0.720 9.250 19943 Z= 0.405 Chirality : 0.046 0.278 2253 Planarity : 0.005 0.059 1485 Dihedral : 30.197 158.606 4239 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.73 % Allowed : 31.42 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 831 helix: 0.51 (0.22), residues: 528 sheet: -3.81 (1.42), residues: 10 loop : -0.95 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 99 TYR 0.028 0.002 TYR G 39 PHE 0.029 0.002 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 0.00342 / 0.17 (13814) covalent geometry : angle 0.72009 / 0.40 (19943) hydrogen bonds : bond 0.06090 / 3.88 ( 658) hydrogen bonds : angle 3.37637 / 2.28 ( 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 434 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 0.324 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: B 35 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8930 (mtp85) REVERT: B 39 ARG cc_start: 0.9349 (mmt-90) cc_final: 0.8968 (tpp80) REVERT: B 44 LYS cc_start: 0.9208 (mttt) cc_final: 0.8790 (mttp) REVERT: B 45 ARG cc_start: 0.8877 (mtp-110) cc_final: 0.8551 (mtp85) REVERT: B 53 GLU cc_start: 0.8515 (tp30) cc_final: 0.8229 (tp30) REVERT: B 63 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 42 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7998 (mtm-85) REVERT: C 71 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7551 (ttp-110) REVERT: C 95 LYS cc_start: 0.9191 (ptpt) cc_final: 0.8660 (pttp) REVERT: C 110 ASN cc_start: 0.9037 (t0) cc_final: 0.8700 (t0) REVERT: C 115 LEU cc_start: 0.9125 (mp) cc_final: 0.8852 (mm) REVERT: D 59 MET cc_start: 0.9686 (mmm) cc_final: 0.9333 (tpp) REVERT: D 64 ASN cc_start: 0.9011 (m-40) cc_final: 0.8631 (m-40) REVERT: D 65 ASP cc_start: 0.8925 (t70) cc_final: 0.8718 (t70) REVERT: D 102 GLU cc_start: 0.7841 (tp30) cc_final: 0.7584 (tp30) REVERT: D 109 SER cc_start: 0.9331 (t) cc_final: 0.8724 (p) REVERT: D 110 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 113 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8801 (mmtm) REVERT: F 25 ASN cc_start: 0.8666 (m-40) cc_final: 0.8370 (m-40) REVERT: F 31 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: F 36 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.7502 (mtm-85) REVERT: F 53 GLU cc_start: 0.8656 (tp30) cc_final: 0.8194 (tp30) REVERT: F 63 GLU cc_start: 0.7644 (pp20) cc_final: 0.7014 (pp20) REVERT: F 88 TYR cc_start: 0.9317 (m-10) cc_final: 0.8852 (m-80) REVERT: G 17 ARG cc_start: 0.8511 (mtm180) cc_final: 0.7663 (ptp-170) REVERT: G 42 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.8412 (mtm-85) REVERT: G 58 LEU cc_start: 0.8603 (mt) cc_final: 0.8392 (mp) REVERT: G 61 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8365 (mm-30) REVERT: G 64 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7788 (tm-30) REVERT: G 68 ASN cc_start: 0.8439 (p0) cc_final: 0.8073 (p0) REVERT: G 78 ILE cc_start: 0.8614 (mt) cc_final: 0.8263 (mt) REVERT: G 81 ARG cc_start: 0.8678 (tpt90) cc_final: 0.8435 (tpt90) REVERT: G 89 ASN cc_start: 0.7898 (p0) cc_final: 0.7616 (p0) REVERT: G 95 LYS cc_start: 0.9082 (pttp) cc_final: 0.8785 (pttp) REVERT: G 112 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8575 (mm110) REVERT: H 31 LYS cc_start: 0.8877 (mppt) cc_final: 0.8666 (mppt) REVERT: H 39 TYR cc_start: 0.8359 (t80) cc_final: 0.8123 (t80) REVERT: H 40 LYS cc_start: 0.9493 (tppt) cc_final: 0.8684 (tptp) REVERT: H 43 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7987 (ptpp) REVERT: H 56 MET cc_start: 0.8190 (tmm) cc_final: 0.7892 (tmm) REVERT: H 68 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8365 (mm-30) REVERT: H 73 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8801 (mm-30) REVERT: H 102 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8076 (mm-30) REVERT: H 110 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8468 (tt0) REVERT: H 113 LYS cc_start: 0.9338 (mtmt) cc_final: 0.8990 (ptpt) REVERT: K 40 LEU cc_start: 0.4731 (OUTLIER) cc_final: 0.4348 (tp) REVERT: K 79 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6181 (pt0) REVERT: A 53 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8331 (tmm-80) REVERT: A 56 LYS cc_start: 0.8551 (pttp) cc_final: 0.8139 (pttp) REVERT: A 76 GLN cc_start: 0.8856 (mm110) cc_final: 0.8474 (mm-40) REVERT: A 106 ASP cc_start: 0.8645 (m-30) cc_final: 0.8071 (m-30) REVERT: E 85 GLN cc_start: 0.8100 (mt0) cc_final: 0.7488 (mt0) REVERT: E 99 TYR cc_start: 0.8922 (t80) cc_final: 0.8677 (t80) REVERT: E 105 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7547 (tm-30) REVERT: E 118 THR cc_start: 0.9090 (m) cc_final: 0.8374 (p) REVERT: E 119 ILE cc_start: 0.9002 (pt) cc_final: 0.7843 (pt) REVERT: E 120 MET cc_start: 0.7096 (mtt) cc_final: 0.6513 (mpp) outliers start: 48 outliers final: 36 residues processed: 400 average time/residue: 0.1362 time to fit residues: 72.1514 Evaluate side-chains 410 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 33 LEU 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 D residue 41 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 31 LYS 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 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 84 SER 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 K residue 79 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 73 GLU 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: 20.0000 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 92 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094730 restraints weight = 29639.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097861 restraints weight = 16311.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099862 restraints weight = 11335.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101070 restraints weight = 9074.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101813 restraints weight = 7968.387| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13814 Z= 0.218 Angle : 0.745 8.244 19943 Z= 0.415 Chirality : 0.047 0.308 2253 Planarity : 0.006 0.058 1485 Dihedral : 30.213 157.877 4239 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 7.29 % Allowed : 32.54 % Favored : 60.17 % 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: 0.60 (0.22), residues: 530 sheet: -3.74 (1.45), residues: 10 loop : -0.86 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 35 TYR 0.024 0.002 TYR G 39 PHE 0.017 0.002 PHE F 61 TRP 0.003 0.001 TRP K 82 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (13814) covalent geometry : angle 0.74550 / 0.41 (19943) hydrogen bonds : bond 0.06306 / 4.06 ( 658) hydrogen bonds : angle 3.52636 / 2.38 ( 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 428 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 376 time to evaluate : 0.242 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 35 ARG cc_start: 0.9243 (mtp85) cc_final: 0.8884 (ttm110) REVERT: B 44 LYS cc_start: 0.9354 (mttt) cc_final: 0.8690 (mttp) REVERT: B 45 ARG cc_start: 0.8986 (mtp-110) cc_final: 0.8592 (mtp85) REVERT: B 53 GLU cc_start: 0.8552 (tp30) cc_final: 0.8239 (tp30) REVERT: B 63 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7796 (mt-10) REVERT: B 79 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8736 (mmmm) REVERT: C 20 ARG cc_start: 0.8628 (mmp80) cc_final: 0.8146 (mmt-90) REVERT: C 24 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8004 (mm-40) REVERT: C 71 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7669 (ttp-110) REVERT: C 75 LYS cc_start: 0.9064 (mmtm) cc_final: 0.8726 (mmmm) REVERT: C 95 LYS cc_start: 0.9234 (ptpt) cc_final: 0.8824 (pttp) REVERT: C 110 ASN cc_start: 0.9021 (t0) cc_final: 0.8726 (t0) REVERT: C 115 LEU cc_start: 0.9088 (mp) cc_final: 0.8624 (mt) REVERT: D 59 MET cc_start: 0.9717 (mmm) cc_final: 0.9360 (tpp) REVERT: D 64 ASN cc_start: 0.8912 (m-40) cc_final: 0.8627 (m-40) REVERT: D 102 GLU cc_start: 0.7953 (tp30) cc_final: 0.7635 (tp30) REVERT: D 109 SER cc_start: 0.9361 (t) cc_final: 0.8936 (p) REVERT: D 110 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8068 (mt-10) REVERT: F 45 ARG cc_start: 0.9182 (mtp180) cc_final: 0.8917 (mtp85) REVERT: F 88 TYR cc_start: 0.9341 (m-10) cc_final: 0.8763 (m-80) REVERT: G 17 ARG cc_start: 0.8744 (mtm180) cc_final: 0.7968 (ptp-170) REVERT: G 42 ARG cc_start: 0.8781 (mtp-110) cc_final: 0.8482 (mtp-110) REVERT: G 61 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8033 (mm-30) REVERT: G 64 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7852 (tm-30) REVERT: G 68 ASN cc_start: 0.8360 (p0) cc_final: 0.7867 (p0) REVERT: G 78 ILE cc_start: 0.8866 (mt) cc_final: 0.8583 (mt) REVERT: G 81 ARG cc_start: 0.8792 (tpt90) cc_final: 0.8549 (tpt90) REVERT: G 89 ASN cc_start: 0.7934 (p0) cc_final: 0.7673 (p0) REVERT: G 95 LYS cc_start: 0.9064 (pttp) cc_final: 0.8755 (pttp) REVERT: G 112 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8551 (mm110) REVERT: H 31 LYS cc_start: 0.8924 (mppt) cc_final: 0.8700 (mppt) REVERT: H 40 LYS cc_start: 0.9490 (tppt) cc_final: 0.8689 (tptp) REVERT: H 43 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8034 (ptpp) REVERT: H 56 MET cc_start: 0.8188 (tmm) cc_final: 0.7856 (tmm) REVERT: H 73 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8914 (mm-30) REVERT: H 102 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8048 (mm-30) REVERT: H 110 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8533 (tt0) REVERT: H 113 LYS cc_start: 0.9355 (mtmt) cc_final: 0.9010 (ptpt) REVERT: K 40 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4390 (tp) REVERT: K 79 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6220 (pt0) REVERT: A 53 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8342 (tmm-80) REVERT: A 56 LYS cc_start: 0.8567 (pttp) cc_final: 0.8154 (pttp) REVERT: A 76 GLN cc_start: 0.8878 (mm110) cc_final: 0.8519 (mm-40) REVERT: A 79 LYS cc_start: 0.9068 (tptp) cc_final: 0.8814 (tptp) REVERT: A 106 ASP cc_start: 0.8544 (m-30) cc_final: 0.8198 (m-30) REVERT: E 39 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6839 (p-80) REVERT: E 49 ARG cc_start: 0.8570 (ptm160) cc_final: 0.8022 (ptp90) REVERT: E 60 LEU cc_start: 0.9015 (mm) cc_final: 0.8498 (mm) REVERT: E 63 ARG cc_start: 0.7852 (mmp80) cc_final: 0.7360 (mmp80) REVERT: E 67 PHE cc_start: 0.8990 (t80) cc_final: 0.8644 (t80) REVERT: E 68 GLN cc_start: 0.8623 (pp30) cc_final: 0.8107 (pp30) REVERT: E 78 PHE cc_start: 0.8623 (m-80) cc_final: 0.8372 (m-80) REVERT: E 85 GLN cc_start: 0.8225 (mt0) cc_final: 0.7506 (mt0) REVERT: E 105 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7608 (tm-30) REVERT: E 118 THR cc_start: 0.9043 (m) cc_final: 0.8391 (p) REVERT: E 119 ILE cc_start: 0.8942 (pt) cc_final: 0.7913 (pt) REVERT: E 120 MET cc_start: 0.7283 (mtt) cc_final: 0.6724 (mpp) outliers start: 52 outliers final: 41 residues processed: 387 average time/residue: 0.1302 time to fit residues: 66.7993 Evaluate side-chains 412 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 84 MET Chi-restraints excluded: chain B residue 91 LYS 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 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 92 GLN 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 38 ASN 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 49 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 SER 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 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 101 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 57 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 92 GLN G 73 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095964 restraints weight = 29462.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099153 restraints weight = 16098.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101181 restraints weight = 11158.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102475 restraints weight = 8934.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103273 restraints weight = 7815.975| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13814 Z= 0.160 Angle : 0.718 9.758 19943 Z= 0.403 Chirality : 0.046 0.277 2253 Planarity : 0.006 0.079 1485 Dihedral : 30.163 157.451 4239 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.75 % Allowed : 35.90 % Favored : 58.35 % 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: 0.18 (0.28), residues: 831 helix: 0.71 (0.22), residues: 528 sheet: -3.60 (1.47), residues: 10 loop : -0.68 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 35 TYR 0.033 0.002 TYR G 39 PHE 0.029 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (13814) covalent geometry : angle 0.71833 / 0.40 (19943) hydrogen bonds : bond 0.05792 / 3.69 ( 658) hydrogen bonds : angle 3.37405 / 2.29 ( 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 424 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 0.305 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 31 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8829 (ttmm) REVERT: B 35 ARG cc_start: 0.9216 (mtp85) cc_final: 0.8886 (ttp-110) REVERT: B 44 LYS cc_start: 0.9283 (mttt) cc_final: 0.8538 (mttt) REVERT: B 45 ARG cc_start: 0.9143 (mtp-110) cc_final: 0.8718 (mtp85) REVERT: B 53 GLU cc_start: 0.8468 (tp30) cc_final: 0.8127 (tp30) REVERT: B 61 PHE cc_start: 0.8970 (t80) cc_final: 0.8736 (t80) REVERT: B 63 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7712 (mt-10) REVERT: C 20 ARG cc_start: 0.8565 (mmp80) cc_final: 0.8174 (mmt-90) REVERT: C 75 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8456 (mmmm) REVERT: C 84 GLN cc_start: 0.9269 (tp40) cc_final: 0.9061 (tp-100) REVERT: C 89 ASN cc_start: 0.8787 (m-40) cc_final: 0.8476 (m110) REVERT: C 95 LYS cc_start: 0.9213 (ptpt) cc_final: 0.8765 (pttp) REVERT: C 110 ASN cc_start: 0.8942 (t0) cc_final: 0.8651 (t0) REVERT: C 115 LEU cc_start: 0.9081 (mp) cc_final: 0.8600 (mt) REVERT: D 43 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8656 (tppt) REVERT: D 59 MET cc_start: 0.9685 (mmm) cc_final: 0.9428 (tpp) REVERT: D 64 ASN cc_start: 0.8989 (m-40) cc_final: 0.8474 (m110) REVERT: D 102 GLU cc_start: 0.7886 (tp30) cc_final: 0.7558 (tp30) REVERT: D 109 SER cc_start: 0.9096 (t) cc_final: 0.8587 (p) REVERT: D 110 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8073 (mt-10) REVERT: D 117 LYS cc_start: 0.9231 (tttt) cc_final: 0.8915 (tttp) REVERT: F 45 ARG cc_start: 0.9189 (mtp180) cc_final: 0.8903 (mtp85) REVERT: F 63 GLU cc_start: 0.7713 (pp20) cc_final: 0.6971 (pp20) REVERT: F 88 TYR cc_start: 0.9313 (m-10) cc_final: 0.8859 (m-80) REVERT: F 92 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8431 (mmm-85) REVERT: G 24 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6989 (mm-40) REVERT: G 61 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7941 (mm-30) REVERT: G 64 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7803 (tm-30) REVERT: G 68 ASN cc_start: 0.8379 (p0) cc_final: 0.7851 (p0) REVERT: G 78 ILE cc_start: 0.8860 (mt) cc_final: 0.8584 (mt) REVERT: G 89 ASN cc_start: 0.7720 (p0) cc_final: 0.7453 (p0) REVERT: G 95 LYS cc_start: 0.9036 (pttp) cc_final: 0.8657 (ptpp) REVERT: G 112 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8447 (mm110) REVERT: G 116 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8061 (mt) REVERT: H 31 LYS cc_start: 0.8849 (mppt) cc_final: 0.8612 (mppt) REVERT: H 40 LYS cc_start: 0.9395 (tppt) cc_final: 0.8702 (tptt) REVERT: H 43 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7989 (ptpp) REVERT: H 56 MET cc_start: 0.8056 (tmm) cc_final: 0.7764 (tmm) REVERT: H 73 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8866 (mm-30) REVERT: H 76 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8455 (mtm-85) REVERT: H 84 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (p) REVERT: H 102 GLU cc_start: 0.9001 (mm-30) cc_final: 0.7950 (mm-30) REVERT: H 110 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8513 (tt0) REVERT: H 113 LYS cc_start: 0.9346 (mtmt) cc_final: 0.8991 (ptpt) REVERT: K 40 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4564 (tp) REVERT: K 79 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6219 (pt0) REVERT: A 76 GLN cc_start: 0.8870 (mm110) cc_final: 0.8527 (mm-40) REVERT: A 106 ASP cc_start: 0.8588 (m-30) cc_final: 0.8242 (m-30) REVERT: E 39 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6842 (p-80) REVERT: E 49 ARG cc_start: 0.8548 (ptm160) cc_final: 0.7980 (ptp90) REVERT: E 60 LEU cc_start: 0.8968 (mm) cc_final: 0.8346 (tt) REVERT: E 63 ARG cc_start: 0.7833 (mmp80) cc_final: 0.7389 (mmp80) REVERT: E 64 LYS cc_start: 0.8625 (mmmt) cc_final: 0.7164 (mmmt) REVERT: E 68 GLN cc_start: 0.8641 (pp30) cc_final: 0.8388 (pp30) REVERT: E 85 GLN cc_start: 0.8206 (mt0) cc_final: 0.7543 (mt0) REVERT: E 105 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7620 (tm-30) REVERT: E 117 VAL cc_start: 0.9293 (t) cc_final: 0.9040 (p) REVERT: E 118 THR cc_start: 0.9057 (m) cc_final: 0.8510 (p) REVERT: E 120 MET cc_start: 0.7200 (mtt) cc_final: 0.6658 (mpp) outliers start: 41 outliers final: 27 residues processed: 394 average time/residue: 0.1272 time to fit residues: 66.9109 Evaluate side-chains 406 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 31 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 116 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 84 SER 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 46 VAL 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 57 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 108 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 54 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 73 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096123 restraints weight = 29289.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099286 restraints weight = 16099.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.101304 restraints weight = 11164.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102580 restraints weight = 8944.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103344 restraints weight = 7816.004| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13814 Z= 0.159 Angle : 0.731 11.654 19943 Z= 0.407 Chirality : 0.045 0.271 2253 Planarity : 0.005 0.062 1485 Dihedral : 30.139 157.412 4239 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.63 % Allowed : 38.57 % Favored : 56.80 % 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: 0.32 (0.28), residues: 831 helix: 0.82 (0.22), residues: 527 sheet: -3.51 (1.49), residues: 10 loop : -0.63 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 81 TYR 0.027 0.002 TYR G 39 PHE 0.029 0.001 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (13814) covalent geometry : angle 0.73098 / 0.41 (19943) hydrogen bonds : bond 0.05701 / 3.62 ( 658) hydrogen bonds : angle 3.37315 / 2.28 ( 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 412 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 379 time to evaluate : 0.231 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: B 35 ARG cc_start: 0.9183 (mtp85) cc_final: 0.8797 (ttm110) REVERT: B 44 LYS cc_start: 0.9305 (mttt) cc_final: 0.8521 (mttt) REVERT: B 45 ARG cc_start: 0.9070 (mtp-110) cc_final: 0.8660 (mtp85) REVERT: B 53 GLU cc_start: 0.8492 (tp30) cc_final: 0.8125 (tp30) REVERT: B 63 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 17 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8365 (mtm110) REVERT: C 20 ARG cc_start: 0.8681 (mmp80) cc_final: 0.8258 (mmt-90) REVERT: C 75 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8416 (mmmm) REVERT: C 89 ASN cc_start: 0.8798 (m-40) cc_final: 0.8518 (m110) REVERT: C 95 LYS cc_start: 0.9184 (ptpt) cc_final: 0.8817 (pttp) REVERT: C 110 ASN cc_start: 0.8994 (t0) cc_final: 0.8648 (t0) REVERT: C 115 LEU cc_start: 0.9066 (mp) cc_final: 0.8758 (mm) REVERT: D 43 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8740 (tppt) REVERT: D 59 MET cc_start: 0.9679 (mmm) cc_final: 0.9237 (tpp) REVERT: D 64 ASN cc_start: 0.8941 (m-40) cc_final: 0.8686 (m-40) REVERT: D 102 GLU cc_start: 0.7890 (tp30) cc_final: 0.7664 (tp30) REVERT: D 109 SER cc_start: 0.9118 (t) cc_final: 0.8626 (p) REVERT: D 110 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 117 LYS cc_start: 0.9221 (tttt) cc_final: 0.8911 (tttp) REVERT: F 50 ILE cc_start: 0.8758 (mm) cc_final: 0.8529 (mt) REVERT: F 63 GLU cc_start: 0.7737 (pp20) cc_final: 0.6760 (pp20) REVERT: F 88 TYR cc_start: 0.9277 (m-10) cc_final: 0.8853 (m-80) REVERT: F 92 ARG cc_start: 0.8880 (mmm160) cc_final: 0.8416 (mmm-85) REVERT: G 61 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8081 (mm-30) REVERT: G 64 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7844 (tm-30) REVERT: G 68 ASN cc_start: 0.8418 (p0) cc_final: 0.7879 (p0) REVERT: G 78 ILE cc_start: 0.8880 (mt) cc_final: 0.8608 (mt) REVERT: G 95 LYS cc_start: 0.9040 (pttp) cc_final: 0.8717 (pttp) REVERT: G 112 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8422 (mm110) REVERT: G 116 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8042 (mt) REVERT: H 31 LYS cc_start: 0.8850 (mppt) cc_final: 0.8597 (mppt) REVERT: H 40 LYS cc_start: 0.9401 (tppt) cc_final: 0.8825 (tptt) REVERT: H 43 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8012 (ptpt) REVERT: H 48 ASP cc_start: 0.8767 (m-30) cc_final: 0.8223 (p0) REVERT: H 56 MET cc_start: 0.8078 (tmm) cc_final: 0.7773 (tmm) REVERT: H 73 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8837 (mm-30) REVERT: H 102 GLU cc_start: 0.8976 (mm-30) cc_final: 0.7947 (mm-30) REVERT: H 110 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8330 (tt0) REVERT: H 113 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8984 (ptpt) REVERT: K 79 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6221 (pt0) REVERT: A 56 LYS cc_start: 0.8493 (pttp) cc_final: 0.8053 (pttp) REVERT: A 76 GLN cc_start: 0.8873 (mm110) cc_final: 0.8525 (mm-40) REVERT: A 106 ASP cc_start: 0.8584 (m-30) cc_final: 0.8284 (m-30) REVERT: E 39 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6835 (p-80) REVERT: E 60 LEU cc_start: 0.8960 (mm) cc_final: 0.8330 (mm) REVERT: E 63 ARG cc_start: 0.7838 (mmp80) cc_final: 0.7516 (mmp80) REVERT: E 64 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8235 (mmmt) REVERT: E 68 GLN cc_start: 0.8626 (pp30) cc_final: 0.8199 (pp30) REVERT: E 85 GLN cc_start: 0.8166 (mt0) cc_final: 0.7490 (mt0) REVERT: E 93 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7585 (tm-30) REVERT: E 105 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 118 THR cc_start: 0.9038 (m) cc_final: 0.8377 (p) REVERT: E 120 MET cc_start: 0.7235 (mtt) cc_final: 0.6750 (mpp) outliers start: 33 outliers final: 28 residues processed: 389 average time/residue: 0.1279 time to fit residues: 66.3285 Evaluate side-chains 403 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 97 LEU 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 F residue 31 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 100 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 84 SER 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 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 46 VAL 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 73 GLU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094221 restraints weight = 29916.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097315 restraints weight = 16792.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099336 restraints weight = 11770.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.100611 restraints weight = 9454.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101369 restraints weight = 8283.042| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13814 Z= 0.174 Angle : 0.744 11.657 19943 Z= 0.412 Chirality : 0.045 0.265 2253 Planarity : 0.005 0.063 1485 Dihedral : 30.146 157.067 4237 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.47 % Allowed : 38.15 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.28), residues: 831 helix: 0.83 (0.22), residues: 531 sheet: -3.39 (1.48), residues: 10 loop : -0.56 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.029 0.002 TYR G 39 PHE 0.031 0.002 PHE A 67 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 0.00361 / 0.17 (13814) covalent geometry : angle 0.74401 / 0.41 (19943) hydrogen bonds : bond 0.05814 / 3.72 ( 658) hydrogen bonds : angle 3.36692 / 2.27 ( 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 423 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 384 time to evaluate : 0.196 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 35 ARG cc_start: 0.9182 (mtp85) cc_final: 0.8904 (ttp-110) REVERT: B 44 LYS cc_start: 0.9318 (mttt) cc_final: 0.8751 (mttp) REVERT: B 45 ARG cc_start: 0.9099 (mtp-110) cc_final: 0.8737 (mtp85) REVERT: B 53 GLU cc_start: 0.8491 (tp30) cc_final: 0.8116 (tp30) REVERT: B 63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 17 ARG cc_start: 0.8973 (mtm180) cc_final: 0.8396 (mtm110) REVERT: C 32 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7897 (tmm-80) REVERT: C 75 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8421 (mmmm) REVERT: C 89 ASN cc_start: 0.8814 (m-40) cc_final: 0.8523 (m110) REVERT: C 95 LYS cc_start: 0.9162 (ptpt) cc_final: 0.8947 (pttp) REVERT: C 110 ASN cc_start: 0.9065 (t0) cc_final: 0.8768 (t0) REVERT: C 115 LEU cc_start: 0.9020 (mp) cc_final: 0.8508 (mt) REVERT: D 43 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8808 (tppt) REVERT: D 64 ASN cc_start: 0.9085 (m-40) cc_final: 0.8624 (m110) REVERT: D 92 GLN cc_start: 0.8512 (pt0) cc_final: 0.7949 (pp30) REVERT: D 109 SER cc_start: 0.9337 (t) cc_final: 0.8890 (p) REVERT: F 50 ILE cc_start: 0.8780 (mm) cc_final: 0.8517 (mt) REVERT: F 53 GLU cc_start: 0.8168 (tp30) cc_final: 0.7946 (tp30) REVERT: F 63 GLU cc_start: 0.7754 (pp20) cc_final: 0.6845 (pp20) REVERT: F 88 TYR cc_start: 0.9305 (m-10) cc_final: 0.8727 (m-80) REVERT: G 42 ARG cc_start: 0.8859 (mtp-110) cc_final: 0.7248 (mtm-85) REVERT: G 61 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8087 (mm-30) REVERT: G 68 ASN cc_start: 0.8437 (p0) cc_final: 0.7915 (p0) REVERT: G 78 ILE cc_start: 0.8892 (mt) cc_final: 0.8646 (mt) REVERT: G 85 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8785 (mt) REVERT: G 90 ASP cc_start: 0.8095 (t70) cc_final: 0.7545 (t70) REVERT: G 95 LYS cc_start: 0.8996 (pttp) cc_final: 0.8683 (pttp) REVERT: G 112 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8465 (mm110) REVERT: G 116 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8275 (mt) REVERT: H 31 LYS cc_start: 0.8871 (mppt) cc_final: 0.8620 (mppt) REVERT: H 40 LYS cc_start: 0.9379 (tppt) cc_final: 0.8895 (tmtt) REVERT: H 43 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7987 (ptpt) REVERT: H 48 ASP cc_start: 0.8756 (m-30) cc_final: 0.8264 (p0) REVERT: H 56 MET cc_start: 0.8094 (tmm) cc_final: 0.7799 (tmm) REVERT: H 73 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8745 (mm-30) REVERT: H 76 ARG cc_start: 0.9047 (mtm110) cc_final: 0.8694 (mtm110) REVERT: H 113 LYS cc_start: 0.9340 (mtmt) cc_final: 0.9029 (ptpt) REVERT: K 79 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6233 (pt0) REVERT: A 42 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7053 (mmm-85) REVERT: A 76 GLN cc_start: 0.8879 (mm110) cc_final: 0.8523 (mm-40) REVERT: A 106 ASP cc_start: 0.8548 (m-30) cc_final: 0.8128 (m-30) REVERT: E 39 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6927 (p-80) REVERT: E 49 ARG cc_start: 0.8475 (ptm160) cc_final: 0.7859 (ptp90) REVERT: E 60 LEU cc_start: 0.9042 (mm) cc_final: 0.8473 (mm) REVERT: E 63 ARG cc_start: 0.7770 (mmp80) cc_final: 0.7569 (mmp80) REVERT: E 64 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8314 (mmmt) REVERT: E 68 GLN cc_start: 0.8619 (pp30) cc_final: 0.8377 (pp30) REVERT: E 73 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: E 76 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8702 (tm-30) REVERT: E 85 GLN cc_start: 0.8378 (mt0) cc_final: 0.8077 (mt0) REVERT: E 93 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7549 (tm-30) REVERT: E 105 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 118 THR cc_start: 0.9012 (m) cc_final: 0.8511 (p) REVERT: E 120 MET cc_start: 0.7388 (mtt) cc_final: 0.6894 (mpp) REVERT: E 125 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8167 (mp10) outliers start: 39 outliers final: 32 residues processed: 393 average time/residue: 0.1296 time to fit residues: 67.9039 Evaluate side-chains 412 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 374 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU 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 97 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 31 LYS 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 38 ASN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 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 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU 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 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 100 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 46 HIS ** 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 = 0.3986 r_free = 0.3986 target = 0.138727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093771 restraints weight = 29962.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096887 restraints weight = 16782.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098902 restraints weight = 11725.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100164 restraints weight = 9392.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100943 restraints weight = 8222.374| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13814 Z= 0.182 Angle : 0.769 18.054 19943 Z= 0.423 Chirality : 0.046 0.267 2253 Planarity : 0.005 0.063 1485 Dihedral : 30.148 156.903 4237 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.19 % Allowed : 38.99 % Favored : 55.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.28), residues: 831 helix: 0.75 (0.22), residues: 531 sheet: -3.38 (1.45), residues: 10 loop : -0.51 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 92 TYR 0.023 0.002 TYR G 39 PHE 0.028 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (13814) covalent geometry : angle 0.76885 / 0.42 (19943) hydrogen bonds : bond 0.05799 / 3.70 ( 658) hydrogen bonds : angle 3.42909 / 2.30 ( 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 413 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 0.232 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 31 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9077 (tptp) REVERT: B 44 LYS cc_start: 0.9344 (mttt) cc_final: 0.8719 (mttp) REVERT: B 53 GLU cc_start: 0.8509 (tp30) cc_final: 0.8131 (tp30) REVERT: B 63 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 17 ARG cc_start: 0.9001 (mtm180) cc_final: 0.8399 (mtm110) REVERT: C 20 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8625 (mmt-90) REVERT: C 32 ARG cc_start: 0.8266 (tmm-80) cc_final: 0.7996 (tmm-80) REVERT: C 75 LYS cc_start: 0.8914 (mmtm) cc_final: 0.8465 (mmmm) REVERT: C 89 ASN cc_start: 0.8771 (m-40) cc_final: 0.8506 (m110) REVERT: C 95 LYS cc_start: 0.9174 (ptpt) cc_final: 0.8889 (pttm) REVERT: C 110 ASN cc_start: 0.9101 (t0) cc_final: 0.8824 (t0) REVERT: D 43 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8831 (tppt) REVERT: D 64 ASN cc_start: 0.9044 (m-40) cc_final: 0.8614 (m110) REVERT: D 92 GLN cc_start: 0.8523 (pt0) cc_final: 0.7637 (pp30) REVERT: D 102 GLU cc_start: 0.7790 (tp30) cc_final: 0.7582 (tp30) REVERT: D 109 SER cc_start: 0.9159 (t) cc_final: 0.8800 (p) REVERT: D 117 LYS cc_start: 0.9208 (tttt) cc_final: 0.8835 (ttpp) REVERT: F 44 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8756 (mtmm) REVERT: F 50 ILE cc_start: 0.8786 (mm) cc_final: 0.8534 (mt) REVERT: F 53 GLU cc_start: 0.8217 (tp30) cc_final: 0.7892 (tp30) REVERT: F 63 GLU cc_start: 0.7754 (pp20) cc_final: 0.6867 (pp20) REVERT: F 88 TYR cc_start: 0.9317 (m-10) cc_final: 0.8762 (m-80) REVERT: G 24 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7373 (mp10) REVERT: G 42 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: G 61 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8228 (mm-30) REVERT: G 68 ASN cc_start: 0.8359 (p0) cc_final: 0.8117 (p0) REVERT: G 78 ILE cc_start: 0.8964 (mt) cc_final: 0.8697 (mt) REVERT: G 79 ILE cc_start: 0.8700 (mm) cc_final: 0.8440 (mm) REVERT: G 81 ARG cc_start: 0.8736 (tpt90) cc_final: 0.7969 (tpt90) REVERT: G 85 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8875 (mt) REVERT: G 90 ASP cc_start: 0.8043 (t70) cc_final: 0.7541 (t70) REVERT: G 95 LYS cc_start: 0.9006 (pttp) cc_final: 0.8702 (pttp) REVERT: G 112 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8460 (mm110) REVERT: G 116 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8297 (mt) REVERT: H 31 LYS cc_start: 0.8863 (mppt) cc_final: 0.8614 (mppt) REVERT: H 40 LYS cc_start: 0.9380 (tppt) cc_final: 0.9163 (tmtt) REVERT: H 48 ASP cc_start: 0.8692 (m-30) cc_final: 0.8233 (p0) REVERT: H 56 MET cc_start: 0.8118 (tmm) cc_final: 0.7877 (tmm) REVERT: H 113 LYS cc_start: 0.9321 (mtmt) cc_final: 0.8999 (ptpt) REVERT: K 79 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6249 (pt0) REVERT: A 42 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6948 (mmm-85) REVERT: A 76 GLN cc_start: 0.8848 (mm110) cc_final: 0.8521 (mm-40) REVERT: A 106 ASP cc_start: 0.8441 (m-30) cc_final: 0.8074 (m-30) REVERT: E 39 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6945 (p-80) REVERT: E 60 LEU cc_start: 0.9079 (mm) cc_final: 0.8567 (mm) REVERT: E 64 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8109 (mmmt) REVERT: E 68 GLN cc_start: 0.8573 (pp30) cc_final: 0.8316 (pp30) REVERT: E 73 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: E 76 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8653 (tm-30) REVERT: E 85 GLN cc_start: 0.8414 (mt0) cc_final: 0.8120 (mt0) REVERT: E 93 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7671 (tm-30) REVERT: E 105 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7574 (tm-30) REVERT: E 118 THR cc_start: 0.9149 (m) cc_final: 0.8468 (p) REVERT: E 120 MET cc_start: 0.7368 (mtt) cc_final: 0.6915 (mpp) outliers start: 37 outliers final: 28 residues processed: 384 average time/residue: 0.1296 time to fit residues: 66.5592 Evaluate side-chains 399 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 366 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 97 LEU 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 F residue 31 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 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 65 LYS Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 89 VAL 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 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 107 THR 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: 0.8980 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094434 restraints weight = 30528.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097416 restraints weight = 17197.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099433 restraints weight = 12058.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100603 restraints weight = 9625.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101299 restraints weight = 8433.723| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13814 Z= 0.231 Angle : 0.812 17.893 19943 Z= 0.442 Chirality : 0.047 0.261 2253 Planarity : 0.006 0.072 1485 Dihedral : 30.239 156.619 4237 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 6.31 % Allowed : 38.01 % Favored : 55.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.28), residues: 831 helix: 0.52 (0.22), residues: 531 sheet: -3.38 (1.38), residues: 10 loop : -0.54 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 63 TYR 0.031 0.003 TYR C 57 PHE 0.023 0.002 PHE B 61 TRP 0.003 0.000 TRP K 82 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (13814) covalent geometry : angle 0.81188 / 0.44 (19943) hydrogen bonds : bond 0.06189 / 3.99 ( 658) hydrogen bonds : angle 3.68128 / 2.49 ( 1637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.82 seconds wall clock time: 40 minutes 48.48 seconds (2448.48 seconds total)