Starting phenix.real_space_refine on Fri Sep 11 20:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwe_20506/09_2026/6pwe_20506.map" } resolution = 3.95 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= 0.000 sd= 0.004 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 294 5.49 5 S 14 5.16 5 C 6576 2.51 5 N 2231 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11923 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Restraints were copied for chains: E, F, G, H Time building chain proxies: 2.93, per 1000 atoms: 0.25 Number of scatterers: 11923 At special positions: 0 Unit cell: (108.36, 113.4, 120.96, 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 14 16.00 P 294 15.00 O 2808 8.00 N 2231 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 214.3 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 59.4% alpha, 1.6% beta 95 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 removed outlier: 3.841A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.602A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.589A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.533A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.853A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.699A pdb=" N ALA C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.700A pdb=" N ALA C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.690A pdb=" N ILE D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.842A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.601A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.590A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.534A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.854A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.698A pdb=" N ALA G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 3.701A pdb=" N ALA G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.689A pdb=" N ILE H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.787A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.109A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.536A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.395A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77 206 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 225 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 95 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1843 1.32 - 1.44: 4466 1.44 - 1.56: 5815 1.56 - 1.68: 586 1.68 - 1.80: 26 Bond restraints: 12736 Sorted by residual: bond pdb=" C3' DG I 38 " pdb=" O3' DG I 38 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.28e+01 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C3' DA J 16 " pdb=" O3' DA J 16 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.92e+01 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.65e+01 bond pdb=" C3' DA I -55 " pdb=" O3' DA I -55 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.63e+01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16551 1.74 - 3.49: 1750 3.49 - 5.23: 128 5.23 - 6.97: 20 6.97 - 8.71: 12 Bond angle restraints: 18461 Sorted by residual: angle pdb=" O4' DT J 13 " pdb=" C4' DT J 13 " pdb=" C3' DT J 13 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 119.70 125.41 -5.71 1.20e+00 6.94e-01 2.27e+01 angle pdb=" N3 DT J 43 " pdb=" C4 DT J 43 " pdb=" O4 DT J 43 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" C ARG H 30 " pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.76: 5440 31.76 - 63.52: 1415 63.52 - 95.29: 44 95.29 - 127.05: 0 127.05 - 158.81: 3 Dihedral angle restraints: 6902 sinusoidal: 4744 harmonic: 2158 Sorted by residual: dihedral pdb=" CA LYS D 29 " pdb=" C LYS D 29 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta harmonic sigma weight residual -180.00 -127.05 -52.95 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA LYS H 29 " pdb=" C LYS H 29 " pdb=" N ARG H 30 " pdb=" CA ARG H 30 " ideal model delta harmonic sigma weight residual -180.00 -127.10 -52.90 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ARG D 30 " pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1207 0.048 - 0.097: 673 0.097 - 0.145: 174 0.145 - 0.193: 35 0.193 - 0.242: 9 Chirality restraints: 2098 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 -2.49 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL G 106 " pdb=" CA VAL G 106 " pdb=" CG1 VAL G 106 " pdb=" CG2 VAL G 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL C 106 " pdb=" CA VAL C 106 " pdb=" CG1 VAL C 106 " pdb=" CG2 VAL C 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2095 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+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 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 101 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLY H 101 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY H 101 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2734 2.79 - 3.32: 10074 3.32 - 3.85: 22518 3.85 - 4.37: 26262 4.37 - 4.90: 37230 Nonbonded interactions: 98818 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR H 37 " pdb=" OP1 DG I 48 " model vdw 2.281 3.040 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.317 3.120 nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.318 3.120 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.330 2.496 ... (remaining 98813 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 12736 Z= 0.806 Angle : 1.049 8.715 18461 Z= 0.817 Chirality : 0.061 0.242 2098 Planarity : 0.007 0.069 1318 Dihedral : 27.121 158.809 5510 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -6.65 (0.18), residues: 728 helix: -4.66 (0.11), residues: 440 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.018 0.004 TYR F 51 PHE 0.019 0.003 PHE A 104 HIS 0.008 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01024 / 0.81 (12736) covalent geometry : angle 1.04868 / 0.82 (18461) hydrogen bonds : bond 0.31222 / 20.37 ( 431) hydrogen bonds : angle 11.97429 / 8.19 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8106 (mtp-110) REVERT: A 73 GLU cc_start: 0.7194 (tt0) cc_final: 0.6708 (tp30) REVERT: B 31 LYS cc_start: 0.8599 (tttt) cc_final: 0.8095 (mptt) REVERT: B 51 TYR cc_start: 0.8454 (m-80) cc_final: 0.7977 (m-80) REVERT: C 109 ASN cc_start: 0.7058 (t0) cc_final: 0.6806 (m-40) REVERT: D 48 ASP cc_start: 0.8152 (p0) cc_final: 0.7794 (p0) REVERT: D 106 HIS cc_start: 0.7773 (m90) cc_final: 0.7565 (m-70) REVERT: F 80 THR cc_start: 0.8638 (m) cc_final: 0.8279 (p) REVERT: F 84 MET cc_start: 0.6704 (mmm) cc_final: 0.6012 (mmm) REVERT: F 88 TYR cc_start: 0.8433 (m-10) cc_final: 0.7792 (m-80) REVERT: F 98 TYR cc_start: 0.8948 (m-10) cc_final: 0.8635 (m-10) REVERT: H 40 LYS cc_start: 0.9155 (mttt) cc_final: 0.8814 (mtpt) REVERT: H 80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7494 (m-10) REVERT: H 97 LEU cc_start: 0.8873 (mt) cc_final: 0.8649 (mp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1734 time to fit residues: 57.2824 Evaluate side-chains 169 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 60 ASN D 64 ASN G 23 GLN G 88 ASN H 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108333 restraints weight = 23952.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110188 restraints weight = 14206.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111405 restraints weight = 10199.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112125 restraints weight = 8372.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112421 restraints weight = 7494.951| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12736 Z= 0.187 Angle : 0.799 9.047 18461 Z= 0.463 Chirality : 0.055 0.296 2098 Planarity : 0.006 0.057 1318 Dihedral : 31.133 164.701 4040 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.40 % Favored : 95.19 % Rotamer: Outliers : 1.78 % Allowed : 12.78 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -5.13 (0.23), residues: 728 helix: -3.36 (0.17), residues: 446 sheet: None (None), residues: 0 loop : -3.25 (0.29), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 49 TYR 0.026 0.002 TYR B 88 PHE 0.015 0.001 PHE E 104 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.19 (12736) covalent geometry : angle 0.79909 / 0.46 (18461) hydrogen bonds : bond 0.09596 / 6.64 ( 431) hydrogen bonds : angle 4.06481 / 2.75 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8085 (mtp-110) REVERT: A 73 GLU cc_start: 0.7344 (tt0) cc_final: 0.6984 (tp30) REVERT: B 31 LYS cc_start: 0.8846 (tttt) cc_final: 0.8318 (mptt) REVERT: B 82 THR cc_start: 0.8546 (t) cc_final: 0.8099 (m) REVERT: B 88 TYR cc_start: 0.8369 (m-10) cc_final: 0.7977 (m-10) REVERT: B 95 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7888 (ttm110) REVERT: C 109 ASN cc_start: 0.7258 (t0) cc_final: 0.6852 (m-40) REVERT: D 48 ASP cc_start: 0.8062 (p0) cc_final: 0.7657 (p0) REVERT: F 84 MET cc_start: 0.6297 (mmm) cc_final: 0.4745 (tpp) REVERT: F 88 TYR cc_start: 0.8327 (m-10) cc_final: 0.7541 (m-80) REVERT: H 40 LYS cc_start: 0.9091 (mttt) cc_final: 0.8380 (mtpt) REVERT: H 54 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8312 (tptm) REVERT: H 65 ASP cc_start: 0.8594 (t70) cc_final: 0.8221 (t0) REVERT: H 80 TYR cc_start: 0.8061 (m-10) cc_final: 0.7514 (m-10) outliers start: 11 outliers final: 7 residues processed: 197 average time/residue: 0.1194 time to fit residues: 32.1843 Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain H residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 7 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109847 restraints weight = 23968.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111740 restraints weight = 13992.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112953 restraints weight = 9905.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113679 restraints weight = 8085.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114086 restraints weight = 7224.193| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12736 Z= 0.156 Angle : 0.677 6.989 18461 Z= 0.401 Chirality : 0.047 0.296 2098 Planarity : 0.005 0.051 1318 Dihedral : 31.075 161.026 4040 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.75 % Allowed : 16.67 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.98 (0.26), residues: 728 helix: -2.38 (0.21), residues: 456 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 96 TYR 0.027 0.002 TYR F 98 PHE 0.013 0.001 PHE E 104 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 (12736) covalent geometry : angle 0.67679 / 0.40 (18461) hydrogen bonds : bond 0.07419 / 5.09 ( 431) hydrogen bonds : angle 3.21317 / 2.18 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7309 (tt0) cc_final: 0.6977 (tp30) REVERT: B 31 LYS cc_start: 0.8758 (tttt) cc_final: 0.8322 (mptt) REVERT: B 82 THR cc_start: 0.8569 (t) cc_final: 0.8092 (m) REVERT: B 88 TYR cc_start: 0.8307 (m-10) cc_final: 0.7478 (m-10) REVERT: C 101 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8717 (mp) REVERT: C 109 ASN cc_start: 0.7206 (t0) cc_final: 0.6748 (m-40) REVERT: D 48 ASP cc_start: 0.7997 (p0) cc_final: 0.7631 (p0) REVERT: E 66 PRO cc_start: 0.8131 (Cg_endo) cc_final: 0.7914 (Cg_exo) REVERT: F 29 ILE cc_start: 0.8911 (mt) cc_final: 0.8564 (pt) REVERT: F 84 MET cc_start: 0.6428 (mmm) cc_final: 0.4782 (tpp) REVERT: F 88 TYR cc_start: 0.8266 (m-10) cc_final: 0.7604 (m-80) REVERT: F 98 TYR cc_start: 0.9094 (m-80) cc_final: 0.8869 (m-80) REVERT: H 54 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8307 (tptm) REVERT: H 80 TYR cc_start: 0.8033 (m-10) cc_final: 0.7457 (m-10) outliers start: 17 outliers final: 5 residues processed: 187 average time/residue: 0.1253 time to fit residues: 32.2119 Evaluate side-chains 162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 HIS C 83 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS F 75 HIS G 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100050 restraints weight = 25001.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101616 restraints weight = 15809.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102636 restraints weight = 11818.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103289 restraints weight = 9941.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103664 restraints weight = 8990.895| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 12736 Z= 0.433 Angle : 1.008 13.009 18461 Z= 0.539 Chirality : 0.061 0.399 2098 Planarity : 0.008 0.051 1318 Dihedral : 31.631 169.442 4040 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.20 % Favored : 90.52 % Rotamer: Outliers : 6.63 % Allowed : 15.70 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.26), residues: 728 helix: -2.61 (0.21), residues: 446 sheet: None (None), residues: 0 loop : -3.04 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 31 TYR 0.044 0.005 TYR B 51 PHE 0.017 0.003 PHE F 61 HIS 0.015 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00929 / 0.43 (12736) covalent geometry : angle 1.00822 / 0.54 (18461) hydrogen bonds : bond 0.09847 / 6.86 ( 431) hydrogen bonds : angle 4.31288 / 2.94 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7517 (tt0) cc_final: 0.6953 (tp30) REVERT: B 31 LYS cc_start: 0.8789 (tttt) cc_final: 0.8401 (mptt) REVERT: B 59 LYS cc_start: 0.8510 (tttt) cc_final: 0.7993 (tmtt) REVERT: B 88 TYR cc_start: 0.8416 (m-80) cc_final: 0.7827 (m-10) REVERT: D 48 ASP cc_start: 0.8256 (p0) cc_final: 0.7993 (p0) REVERT: E 59 GLU cc_start: 0.8315 (pm20) cc_final: 0.7913 (mt-10) REVERT: H 37 TYR cc_start: 0.8885 (m-80) cc_final: 0.8450 (m-80) outliers start: 41 outliers final: 33 residues processed: 199 average time/residue: 0.1238 time to fit residues: 33.5796 Evaluate side-chains 194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN G 72 ASN G 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106799 restraints weight = 24105.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108558 restraints weight = 14616.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109689 restraints weight = 10667.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110370 restraints weight = 8879.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110743 restraints weight = 8000.599| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12736 Z= 0.156 Angle : 0.675 8.490 18461 Z= 0.398 Chirality : 0.047 0.376 2098 Planarity : 0.005 0.061 1318 Dihedral : 31.164 166.083 4040 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 2.75 % Allowed : 22.65 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.65 (0.26), residues: 728 helix: -2.06 (0.21), residues: 460 sheet: None (None), residues: 0 loop : -2.88 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 30 TYR 0.054 0.003 TYR F 88 PHE 0.010 0.001 PHE E 104 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.16 (12736) covalent geometry : angle 0.67549 / 0.40 (18461) hydrogen bonds : bond 0.06991 / 4.84 ( 431) hydrogen bonds : angle 3.08358 / 2.10 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7430 (tt0) cc_final: 0.6971 (tp30) REVERT: B 31 LYS cc_start: 0.8554 (tttt) cc_final: 0.8333 (mptt) REVERT: B 35 ARG cc_start: 0.8293 (tpp80) cc_final: 0.8012 (ttp80) REVERT: B 88 TYR cc_start: 0.8139 (m-10) cc_final: 0.7573 (m-10) REVERT: C 54 MET cc_start: 0.6864 (mtp) cc_final: 0.6547 (mtm) REVERT: D 48 ASP cc_start: 0.8093 (p0) cc_final: 0.7819 (p0) REVERT: E 59 GLU cc_start: 0.8347 (pm20) cc_final: 0.7919 (mt-10) REVERT: F 88 TYR cc_start: 0.8193 (m-80) cc_final: 0.7918 (m-80) REVERT: H 65 ASP cc_start: 0.8543 (t70) cc_final: 0.8262 (t0) REVERT: H 96 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7555 (mtp85) REVERT: H 98 LEU cc_start: 0.8274 (mp) cc_final: 0.8026 (mp) outliers start: 17 outliers final: 9 residues processed: 179 average time/residue: 0.1259 time to fit residues: 30.5718 Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 91 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102896 restraints weight = 24353.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104575 restraints weight = 15016.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105651 restraints weight = 11045.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106298 restraints weight = 9240.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106681 restraints weight = 8351.975| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12736 Z= 0.268 Angle : 0.773 7.944 18461 Z= 0.433 Chirality : 0.050 0.406 2098 Planarity : 0.005 0.053 1318 Dihedral : 31.301 169.572 4040 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.02 % Allowed : 21.52 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.51 (0.27), residues: 728 helix: -1.90 (0.22), residues: 458 sheet: None (None), residues: 0 loop : -2.91 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 31 TYR 0.028 0.003 TYR F 88 PHE 0.009 0.002 PHE E 104 HIS 0.010 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.27 (12736) covalent geometry : angle 0.77260 / 0.43 (18461) hydrogen bonds : bond 0.07591 / 5.33 ( 431) hydrogen bonds : angle 3.50237 / 2.39 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8581 (mtp-110) cc_final: 0.7910 (mtp85) REVERT: A 73 GLU cc_start: 0.7426 (tt0) cc_final: 0.7010 (tp30) REVERT: B 82 THR cc_start: 0.8563 (t) cc_final: 0.8195 (m) REVERT: B 88 TYR cc_start: 0.8184 (m-10) cc_final: 0.7512 (m-10) REVERT: D 48 ASP cc_start: 0.8258 (p0) cc_final: 0.7968 (p0) REVERT: F 88 TYR cc_start: 0.8350 (m-80) cc_final: 0.8040 (m-80) REVERT: H 37 TYR cc_start: 0.8592 (m-80) cc_final: 0.8346 (m-80) REVERT: H 98 LEU cc_start: 0.8435 (mp) cc_final: 0.8177 (mp) outliers start: 31 outliers final: 26 residues processed: 182 average time/residue: 0.1177 time to fit residues: 29.7037 Evaluate side-chains 184 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN G 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105789 restraints weight = 24224.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107553 restraints weight = 14567.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108705 restraints weight = 10595.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109383 restraints weight = 8772.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109784 restraints weight = 7906.671| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12736 Z= 0.160 Angle : 0.656 8.011 18461 Z= 0.387 Chirality : 0.045 0.386 2098 Planarity : 0.004 0.054 1318 Dihedral : 31.049 168.228 4040 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.56 % Allowed : 22.65 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.11 (0.28), residues: 728 helix: -1.63 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -2.67 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.036 0.003 TYR F 88 PHE 0.007 0.001 PHE E 104 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (12736) covalent geometry : angle 0.65570 / 0.39 (18461) hydrogen bonds : bond 0.06623 / 4.61 ( 431) hydrogen bonds : angle 3.08219 / 2.09 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.7919 (mtp85) REVERT: A 73 GLU cc_start: 0.7426 (tt0) cc_final: 0.6971 (tp30) REVERT: B 82 THR cc_start: 0.8487 (t) cc_final: 0.8090 (m) REVERT: B 88 TYR cc_start: 0.8083 (m-10) cc_final: 0.7503 (m-10) REVERT: C 54 MET cc_start: 0.6909 (mtp) cc_final: 0.6616 (mtm) REVERT: D 48 ASP cc_start: 0.8151 (p0) cc_final: 0.7943 (p0) REVERT: E 59 GLU cc_start: 0.8243 (pm20) cc_final: 0.7990 (mp0) REVERT: H 98 LEU cc_start: 0.8362 (mp) cc_final: 0.8137 (mp) outliers start: 22 outliers final: 16 residues processed: 166 average time/residue: 0.1218 time to fit residues: 28.0579 Evaluate side-chains 161 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 84 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103944 restraints weight = 24243.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105652 restraints weight = 14783.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106768 restraints weight = 10849.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107376 restraints weight = 9031.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107790 restraints weight = 8187.472| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12736 Z= 0.227 Angle : 0.701 6.137 18461 Z= 0.403 Chirality : 0.047 0.398 2098 Planarity : 0.005 0.055 1318 Dihedral : 31.117 169.072 4040 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.85 % Allowed : 22.33 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.01 (0.28), residues: 728 helix: -1.53 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 31 TYR 0.073 0.003 TYR F 88 PHE 0.008 0.001 PHE E 104 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (12736) covalent geometry : angle 0.70117 / 0.40 (18461) hydrogen bonds : bond 0.06940 / 4.86 ( 431) hydrogen bonds : angle 3.29813 / 2.24 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.7908 (mtp85) REVERT: A 73 GLU cc_start: 0.7518 (tt0) cc_final: 0.7033 (tp30) REVERT: B 82 THR cc_start: 0.8537 (t) cc_final: 0.8150 (m) REVERT: B 88 TYR cc_start: 0.8074 (m-10) cc_final: 0.7410 (m-10) REVERT: C 54 MET cc_start: 0.6941 (mtp) cc_final: 0.6652 (mtm) REVERT: E 59 GLU cc_start: 0.8365 (pm20) cc_final: 0.8061 (mp0) REVERT: F 100 PHE cc_start: 0.7980 (m-80) cc_final: 0.7594 (m-80) REVERT: H 98 LEU cc_start: 0.8442 (mp) cc_final: 0.8204 (mp) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.1165 time to fit residues: 27.2221 Evaluate side-chains 171 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107107 restraints weight = 23980.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108866 restraints weight = 14384.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109991 restraints weight = 10448.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110650 restraints weight = 8677.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111042 restraints weight = 7828.064| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12736 Z= 0.149 Angle : 0.629 6.375 18461 Z= 0.373 Chirality : 0.044 0.377 2098 Planarity : 0.004 0.054 1318 Dihedral : 30.923 167.469 4040 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.56 % Allowed : 23.95 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.62 (0.29), residues: 728 helix: -1.27 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.42 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.060 0.002 TYR F 88 PHE 0.015 0.001 PHE G 24 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12736) covalent geometry : angle 0.62885 / 0.37 (18461) hydrogen bonds : bond 0.06315 / 4.38 ( 431) hydrogen bonds : angle 2.97375 / 2.03 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8493 (mtp-110) cc_final: 0.7877 (mtp85) REVERT: A 73 GLU cc_start: 0.7479 (tt0) cc_final: 0.6966 (tp30) REVERT: B 82 THR cc_start: 0.8434 (t) cc_final: 0.8047 (m) REVERT: B 88 TYR cc_start: 0.7968 (m-10) cc_final: 0.7474 (m-10) REVERT: C 54 MET cc_start: 0.6880 (mtp) cc_final: 0.6601 (mtm) REVERT: H 56 MET cc_start: 0.7876 (mmm) cc_final: 0.6951 (mtt) REVERT: H 75 SER cc_start: 0.9093 (t) cc_final: 0.8890 (t) REVERT: H 98 LEU cc_start: 0.8350 (mp) cc_final: 0.8120 (mp) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 0.1172 time to fit residues: 26.6719 Evaluate side-chains 159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107417 restraints weight = 24202.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109166 restraints weight = 14516.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110271 restraints weight = 10561.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110958 restraints weight = 8773.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111354 restraints weight = 7907.358| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12736 Z= 0.149 Angle : 0.634 9.479 18461 Z= 0.372 Chirality : 0.043 0.369 2098 Planarity : 0.004 0.054 1318 Dihedral : 30.880 166.961 4040 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.75 % Allowed : 25.57 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.44 (0.29), residues: 728 helix: -1.11 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -2.43 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.071 0.002 TYR F 88 PHE 0.012 0.001 PHE G 24 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12736) covalent geometry : angle 0.63363 / 0.37 (18461) hydrogen bonds : bond 0.06266 / 4.36 ( 431) hydrogen bonds : angle 2.90910 / 1.98 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8494 (mtp-110) cc_final: 0.7878 (mtp85) REVERT: A 73 GLU cc_start: 0.7461 (tt0) cc_final: 0.6901 (tp30) REVERT: B 59 LYS cc_start: 0.8420 (tttt) cc_final: 0.7852 (tmtt) REVERT: B 82 THR cc_start: 0.8467 (t) cc_final: 0.8054 (m) REVERT: B 88 TYR cc_start: 0.7888 (m-10) cc_final: 0.7331 (m-10) REVERT: C 54 MET cc_start: 0.6874 (mtp) cc_final: 0.6583 (mtm) REVERT: H 31 LYS cc_start: 0.7434 (mmmt) cc_final: 0.6873 (mmmt) REVERT: H 75 SER cc_start: 0.9085 (t) cc_final: 0.8878 (t) REVERT: H 83 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (ttm110) REVERT: H 98 LEU cc_start: 0.8344 (mp) cc_final: 0.8083 (mp) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.1250 time to fit residues: 27.7864 Evaluate side-chains 159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 53 optimal weight: 0.0980 chunk 90 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 50 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109474 restraints weight = 23895.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111300 restraints weight = 14089.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112479 restraints weight = 10112.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113171 restraints weight = 8341.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113539 restraints weight = 7509.339| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12736 Z= 0.139 Angle : 0.602 8.215 18461 Z= 0.359 Chirality : 0.041 0.352 2098 Planarity : 0.004 0.054 1318 Dihedral : 30.706 165.897 4040 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.43 % Allowed : 26.21 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.95 (0.30), residues: 728 helix: -0.79 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -2.11 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.063 0.002 TYR F 88 PHE 0.011 0.001 PHE G 24 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12736) covalent geometry : angle 0.60188 / 0.36 (18461) hydrogen bonds : bond 0.06057 / 4.20 ( 431) hydrogen bonds : angle 2.78830 / 1.91 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.41 seconds wall clock time: 29 minutes 28.83 seconds (1768.83 seconds total)