Starting phenix.real_space_refine on Thu Jul 24 08:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyv_27085/07_2025/8cyv_27085.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 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: 3 Type Number sf(0) Gaussians C 3744 2.51 5 N 1044 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "I" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 497 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, J, K, L, M, N Time building chain proxies: 2.22, per 1000 atoms: 0.37 Number of scatterers: 5964 At special positions: 0 Unit cell: (81, 114.48, 48.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1176 8.00 N 1044 7.00 C 3744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 724.5 milliseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 23 removed outlier: 6.520A pdb=" N VAL C 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA B 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS B 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU C 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS B 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA C 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS C 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU D 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LYS C 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL F 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA E 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA F 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LYS E 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU F 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS E 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42 removed outlier: 6.475A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY B 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.266A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 removed outlier: 6.950A pdb=" N ALA C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA D 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA F 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.778A pdb=" N VAL C 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN C 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN D 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL E 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN F 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.521A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.393A pdb=" N ALA C 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA D 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA F 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.643A pdb=" N ALA C 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA D 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA F 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.609A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 17 through 23 removed outlier: 6.795A pdb=" N ALA K 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS J 21 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU K 20 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS J 23 " --> pdb=" O GLU K 20 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR K 22 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA L 18 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS K 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU L 20 " --> pdb=" O LYS K 21 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LYS K 23 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR L 22 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA N 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LYS M 21 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU N 20 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS M 23 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR N 22 " --> pdb=" O LYS M 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 38 through 42 removed outlier: 6.147A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU L 38 " --> pdb=" O TYR M 39 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY M 41 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL L 40 " --> pdb=" O GLY M 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 48 through 49 removed outlier: 6.453A pdb=" N VAL K 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL L 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL N 48 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 62 through 64 removed outlier: 6.485A pdb=" N VAL K 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL L 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL N 63 " --> pdb=" O THR M 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 70 through 71 removed outlier: 6.107A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL L 70 " --> pdb=" O VAL M 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 75 through 79 removed outlier: 6.226A pdb=" N ALA K 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN J 79 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA K 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA L 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN K 79 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA L 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA N 76 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN M 79 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA N 78 " --> pdb=" O GLN M 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 86 through 91 removed outlier: 6.365A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER L 87 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA M 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA L 89 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 94 through 95 removed outlier: 5.970A pdb=" N PHE K 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE L 94 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE N 94 " --> pdb=" O VAL M 95 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1032 1.29 - 1.36: 924 1.36 - 1.43: 204 1.43 - 1.49: 1080 1.49 - 1.56: 2736 Bond restraints: 5976 Sorted by residual: bond pdb=" N LYS N 58 " pdb=" CA LYS N 58 " ideal model delta sigma weight residual 1.461 1.476 -0.014 1.52e-02 4.33e+03 8.97e-01 bond pdb=" N LYS J 58 " pdb=" CA LYS J 58 " ideal model delta sigma weight residual 1.461 1.475 -0.014 1.52e-02 4.33e+03 8.82e-01 bond pdb=" N LYS I 58 " pdb=" CA LYS I 58 " ideal model delta sigma weight residual 1.461 1.475 -0.014 1.52e-02 4.33e+03 8.40e-01 bond pdb=" N LYS L 58 " pdb=" CA LYS L 58 " ideal model delta sigma weight residual 1.461 1.475 -0.014 1.52e-02 4.33e+03 8.37e-01 bond pdb=" C GLU M 57 " pdb=" N LYS M 58 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.40e-02 5.10e+03 8.21e-01 ... (remaining 5971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 7505 1.03 - 2.06: 411 2.06 - 3.09: 88 3.09 - 4.12: 36 4.12 - 5.15: 12 Bond angle restraints: 8052 Sorted by residual: angle pdb=" C THR D 81 " pdb=" N VAL D 82 " pdb=" CA VAL D 82 " ideal model delta sigma weight residual 121.97 127.12 -5.15 1.80e+00 3.09e-01 8.18e+00 angle pdb=" C THR E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta sigma weight residual 121.97 127.12 -5.15 1.80e+00 3.09e-01 8.18e+00 angle pdb=" C THR F 81 " pdb=" N VAL F 82 " pdb=" CA VAL F 82 " ideal model delta sigma weight residual 121.97 127.11 -5.14 1.80e+00 3.09e-01 8.16e+00 angle pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 121.97 127.11 -5.14 1.80e+00 3.09e-01 8.16e+00 angle pdb=" C THR C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta sigma weight residual 121.97 127.11 -5.14 1.80e+00 3.09e-01 8.14e+00 ... (remaining 8047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 3184 11.63 - 23.26: 271 23.26 - 34.89: 49 34.89 - 46.52: 12 46.52 - 58.15: 12 Dihedral angle restraints: 3528 sinusoidal: 1188 harmonic: 2340 Sorted by residual: dihedral pdb=" CA GLY M 73 " pdb=" C GLY M 73 " pdb=" N VAL M 74 " pdb=" CA VAL M 74 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLY K 73 " pdb=" C GLY K 73 " pdb=" N VAL K 74 " pdb=" CA VAL K 74 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLY I 73 " pdb=" C GLY I 73 " pdb=" N VAL I 74 " pdb=" CA VAL I 74 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 449 0.025 - 0.050: 309 0.050 - 0.075: 103 0.075 - 0.099: 84 0.099 - 0.124: 123 Chirality restraints: 1068 Sorted by residual: chirality pdb=" CA ILE I 88 " pdb=" N ILE I 88 " pdb=" C ILE I 88 " pdb=" CB ILE I 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE L 88 " pdb=" N ILE L 88 " pdb=" C ILE L 88 " pdb=" CB ILE L 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA VAL K 40 " pdb=" N VAL K 40 " pdb=" C VAL K 40 " pdb=" CB VAL K 40 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 1065 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 81 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C THR A 81 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 81 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 82 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 81 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C THR D 81 " 0.030 2.00e-02 2.50e+03 pdb=" O THR D 81 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL D 82 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 81 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C THR E 81 " 0.030 2.00e-02 2.50e+03 pdb=" O THR E 81 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL E 82 " -0.010 2.00e-02 2.50e+03 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2394 2.92 - 3.41: 4632 3.41 - 3.91: 9727 3.91 - 4.40: 9551 4.40 - 4.90: 21742 Nonbonded interactions: 48046 Sorted by model distance: nonbonded pdb=" O THR D 75 " pdb=" OG1 THR D 75 " model vdw 2.423 3.040 nonbonded pdb=" O THR B 75 " pdb=" OG1 THR B 75 " model vdw 2.423 3.040 nonbonded pdb=" O THR A 75 " pdb=" OG1 THR A 75 " model vdw 2.424 3.040 nonbonded pdb=" O THR E 75 " pdb=" OG1 THR E 75 " model vdw 2.424 3.040 nonbonded pdb=" O THR F 75 " pdb=" OG1 THR F 75 " model vdw 2.424 3.040 ... (remaining 48041 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=1.00 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: 4.050 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.480 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.025 5976 Z= 0.160 Angle : 0.611 5.149 8052 Z= 0.358 Chirality : 0.053 0.124 1068 Planarity : 0.003 0.018 984 Dihedral : 10.014 58.153 2040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.23), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.005 0.002 PHE M 94 TYR 0.006 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.16075 ( 114) hydrogen bonds : angle 7.48079 ( 342) covalent geometry : bond 0.00285 ( 5976) covalent geometry : angle 0.61068 ( 8052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.687 Fit side-chains REVERT: A 79 GLN cc_start: 0.8325 (mt0) cc_final: 0.8090 (mt0) REVERT: D 23 LYS cc_start: 0.8155 (tttt) cc_final: 0.7581 (tmtt) REVERT: E 23 LYS cc_start: 0.8225 (tttt) cc_final: 0.7907 (tmtt) REVERT: E 46 GLU cc_start: 0.8186 (tp30) cc_final: 0.7975 (tt0) REVERT: L 43 LYS cc_start: 0.7952 (mttp) cc_final: 0.7617 (mmtp) REVERT: L 46 GLU cc_start: 0.7504 (tt0) cc_final: 0.7279 (tm-30) REVERT: M 43 LYS cc_start: 0.7818 (mttp) cc_final: 0.7587 (mttt) REVERT: K 46 GLU cc_start: 0.7733 (tt0) cc_final: 0.7493 (tm-30) REVERT: J 46 GLU cc_start: 0.7561 (tt0) cc_final: 0.7298 (tm-30) REVERT: J 62 GLN cc_start: 0.7442 (tt0) cc_final: 0.7108 (tm-30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2205 time to fit residues: 40.2277 Evaluate side-chains 117 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN D 62 GLN E 62 GLN I 24 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125459 restraints weight = 8087.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.128983 restraints weight = 3976.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131286 restraints weight = 2404.435| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5976 Z= 0.271 Angle : 0.628 4.954 8052 Z= 0.353 Chirality : 0.051 0.135 1068 Planarity : 0.003 0.015 984 Dihedral : 5.688 18.050 852 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.00 % Allowed : 10.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.23), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.011 0.002 PHE C 94 TYR 0.028 0.005 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.02130 ( 114) hydrogen bonds : angle 5.00026 ( 342) covalent geometry : bond 0.00576 ( 5976) covalent geometry : angle 0.62790 ( 8052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8160 (tttt) cc_final: 0.7603 (tmtt) REVERT: E 58 LYS cc_start: 0.7756 (tptm) cc_final: 0.6855 (mttp) REVERT: E 79 GLN cc_start: 0.8258 (mt0) cc_final: 0.7817 (mt0) REVERT: C 45 LYS cc_start: 0.8358 (mttt) cc_final: 0.7877 (mtpt) REVERT: L 46 GLU cc_start: 0.7211 (tt0) cc_final: 0.6963 (tm-30) REVERT: M 43 LYS cc_start: 0.7783 (mttp) cc_final: 0.7304 (mtpt) REVERT: M 46 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7215 (tm-30) REVERT: K 46 GLU cc_start: 0.7310 (tt0) cc_final: 0.7060 (tm-30) REVERT: J 45 LYS cc_start: 0.8188 (tttt) cc_final: 0.7145 (mttm) REVERT: J 46 GLU cc_start: 0.7513 (tt0) cc_final: 0.6931 (tm-30) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.2325 time to fit residues: 41.7997 Evaluate side-chains 141 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN D 62 GLN D 79 GLN E 62 GLN C 62 GLN C 79 GLN B 79 GLN I 65 ASN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124299 restraints weight = 8743.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.127441 restraints weight = 4379.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.129472 restraints weight = 2670.312| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5976 Z= 0.216 Angle : 0.565 7.574 8052 Z= 0.314 Chirality : 0.051 0.164 1068 Planarity : 0.002 0.021 984 Dihedral : 5.387 20.209 852 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.50 % Allowed : 14.83 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.010 0.002 PHE K 94 TYR 0.018 0.003 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01975 ( 114) hydrogen bonds : angle 4.74271 ( 342) covalent geometry : bond 0.00455 ( 5976) covalent geometry : angle 0.56536 ( 8052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 LYS cc_start: 0.8816 (mttt) cc_final: 0.8239 (mttm) REVERT: F 97 LYS cc_start: 0.6991 (tttt) cc_final: 0.6628 (mttt) REVERT: D 23 LYS cc_start: 0.7863 (tttt) cc_final: 0.7439 (tmtt) REVERT: D 38 LEU cc_start: 0.8588 (mp) cc_final: 0.8338 (mp) REVERT: E 23 LYS cc_start: 0.8096 (tttt) cc_final: 0.7555 (tmtt) REVERT: E 58 LYS cc_start: 0.7648 (tptm) cc_final: 0.6860 (mttp) REVERT: E 79 GLN cc_start: 0.8326 (mt0) cc_final: 0.8090 (mt0) REVERT: C 45 LYS cc_start: 0.8413 (mttt) cc_final: 0.7907 (mtpt) REVERT: L 43 LYS cc_start: 0.8220 (mptt) cc_final: 0.7757 (mmtp) REVERT: M 43 LYS cc_start: 0.7774 (mttp) cc_final: 0.7291 (mtpt) REVERT: M 46 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7272 (tm-30) REVERT: K 46 GLU cc_start: 0.7329 (tt0) cc_final: 0.7033 (tm-30) REVERT: K 65 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7837 (t0) REVERT: J 45 LYS cc_start: 0.8212 (tttt) cc_final: 0.7252 (mttm) REVERT: J 46 GLU cc_start: 0.7509 (tt0) cc_final: 0.7293 (tm-30) outliers start: 21 outliers final: 19 residues processed: 151 average time/residue: 0.2368 time to fit residues: 44.0031 Evaluate side-chains 160 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 65 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN E 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN L 65 ASN L 79 GLN N 79 GLN M 62 GLN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN K 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.122266 restraints weight = 8952.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125217 restraints weight = 4465.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.127276 restraints weight = 2779.790| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5976 Z= 0.228 Angle : 0.580 7.783 8052 Z= 0.322 Chirality : 0.051 0.161 1068 Planarity : 0.003 0.022 984 Dihedral : 5.525 22.670 852 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.17 % Allowed : 17.17 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.011 0.002 PHE E 94 TYR 0.018 0.003 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01908 ( 114) hydrogen bonds : angle 4.73008 ( 342) covalent geometry : bond 0.00477 ( 5976) covalent geometry : angle 0.57951 ( 8052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: F 45 LYS cc_start: 0.8836 (mttt) cc_final: 0.8279 (mttm) REVERT: F 58 LYS cc_start: 0.7999 (tptm) cc_final: 0.7398 (mptt) REVERT: F 97 LYS cc_start: 0.6922 (tttt) cc_final: 0.6593 (mttt) REVERT: D 23 LYS cc_start: 0.7629 (tttt) cc_final: 0.7285 (tmtt) REVERT: E 23 LYS cc_start: 0.8131 (tttt) cc_final: 0.7592 (tmtt) REVERT: E 58 LYS cc_start: 0.7703 (tptm) cc_final: 0.6900 (mttp) REVERT: E 79 GLN cc_start: 0.8365 (mt0) cc_final: 0.8109 (mt0) REVERT: C 45 LYS cc_start: 0.8418 (mttt) cc_final: 0.7897 (mtpt) REVERT: I 65 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8052 (t0) REVERT: L 43 LYS cc_start: 0.8207 (mptt) cc_final: 0.7766 (mmtp) REVERT: L 62 GLN cc_start: 0.8037 (mt0) cc_final: 0.7697 (tt0) REVERT: N 83 GLU cc_start: 0.7849 (tp30) cc_final: 0.7579 (tt0) REVERT: M 43 LYS cc_start: 0.7786 (mttp) cc_final: 0.7280 (mtpt) REVERT: M 46 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7350 (tm-30) REVERT: K 46 GLU cc_start: 0.7068 (tt0) cc_final: 0.6750 (tm-30) outliers start: 25 outliers final: 20 residues processed: 154 average time/residue: 0.2366 time to fit residues: 44.6728 Evaluate side-chains 159 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.117244 restraints weight = 9018.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120005 restraints weight = 4647.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122000 restraints weight = 2975.173| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 5976 Z= 0.403 Angle : 0.793 7.318 8052 Z= 0.441 Chirality : 0.055 0.157 1068 Planarity : 0.004 0.023 984 Dihedral : 6.704 31.652 852 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.00 % Allowed : 18.17 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.20), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.15), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 50 PHE 0.017 0.003 PHE E 94 TYR 0.028 0.004 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 114) hydrogen bonds : angle 5.47582 ( 342) covalent geometry : bond 0.00855 ( 5976) covalent geometry : angle 0.79270 ( 8052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.725 Fit side-chains REVERT: F 45 LYS cc_start: 0.8926 (mttt) cc_final: 0.8366 (mttm) REVERT: F 58 LYS cc_start: 0.8122 (tptm) cc_final: 0.7551 (mptt) REVERT: F 97 LYS cc_start: 0.7074 (tttt) cc_final: 0.6542 (mttm) REVERT: D 23 LYS cc_start: 0.7754 (tttt) cc_final: 0.7392 (tmtt) REVERT: E 23 LYS cc_start: 0.8066 (tttt) cc_final: 0.7527 (tmtt) REVERT: C 45 LYS cc_start: 0.8425 (mttt) cc_final: 0.7933 (mtpt) REVERT: L 62 GLN cc_start: 0.8063 (mt0) cc_final: 0.7625 (tt0) REVERT: N 83 GLU cc_start: 0.7866 (tp30) cc_final: 0.7659 (tt0) REVERT: M 23 LYS cc_start: 0.7613 (mtmt) cc_final: 0.6884 (tptm) REVERT: M 43 LYS cc_start: 0.7844 (mttp) cc_final: 0.7342 (mtpt) REVERT: K 46 GLU cc_start: 0.7210 (tt0) cc_final: 0.6961 (tm-30) outliers start: 36 outliers final: 25 residues processed: 170 average time/residue: 0.2180 time to fit residues: 46.1748 Evaluate side-chains 174 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 79 GLN C 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.137954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.120503 restraints weight = 8745.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.123451 restraints weight = 4420.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.125419 restraints weight = 2736.587| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5976 Z= 0.194 Angle : 0.574 7.699 8052 Z= 0.319 Chirality : 0.052 0.202 1068 Planarity : 0.002 0.020 984 Dihedral : 5.721 22.229 852 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.00 % Allowed : 18.17 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 PHE 0.012 0.002 PHE K 94 TYR 0.016 0.002 TYR M 39 Details of bonding type rmsd hydrogen bonds : bond 0.01896 ( 114) hydrogen bonds : angle 4.90018 ( 342) covalent geometry : bond 0.00401 ( 5976) covalent geometry : angle 0.57421 ( 8052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.641 Fit side-chains REVERT: F 45 LYS cc_start: 0.8861 (mttt) cc_final: 0.8325 (mttm) REVERT: F 97 LYS cc_start: 0.7100 (tttt) cc_final: 0.6621 (mttm) REVERT: D 23 LYS cc_start: 0.7681 (tttt) cc_final: 0.7245 (tmtt) REVERT: E 23 LYS cc_start: 0.8089 (tttt) cc_final: 0.7533 (tmtt) REVERT: E 58 LYS cc_start: 0.7668 (tptm) cc_final: 0.7105 (mttp) REVERT: C 45 LYS cc_start: 0.8368 (mttt) cc_final: 0.7916 (mtpt) REVERT: I 62 GLN cc_start: 0.7804 (mt0) cc_final: 0.7501 (mt0) REVERT: M 43 LYS cc_start: 0.7828 (mttp) cc_final: 0.7357 (mtpt) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 0.2088 time to fit residues: 42.9013 Evaluate side-chains 172 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 79 GLN C 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.136501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.119078 restraints weight = 8868.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.121982 restraints weight = 4466.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.123901 restraints weight = 2762.764| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5976 Z= 0.252 Angle : 0.628 7.826 8052 Z= 0.348 Chirality : 0.052 0.187 1068 Planarity : 0.003 0.020 984 Dihedral : 5.918 26.222 852 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 6.67 % Allowed : 18.00 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 50 PHE 0.015 0.002 PHE E 94 TYR 0.018 0.003 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02132 ( 114) hydrogen bonds : angle 5.02636 ( 342) covalent geometry : bond 0.00531 ( 5976) covalent geometry : angle 0.62776 ( 8052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.731 Fit side-chains REVERT: F 45 LYS cc_start: 0.8897 (mttt) cc_final: 0.8609 (mttp) REVERT: F 97 LYS cc_start: 0.7147 (tttt) cc_final: 0.6580 (mttm) REVERT: D 23 LYS cc_start: 0.7615 (tttt) cc_final: 0.7167 (tmtt) REVERT: E 23 LYS cc_start: 0.8019 (tttt) cc_final: 0.7432 (tmtt) REVERT: C 38 LEU cc_start: 0.8506 (mt) cc_final: 0.8249 (mt) REVERT: C 45 LYS cc_start: 0.8320 (mttt) cc_final: 0.7921 (mtpt) REVERT: M 43 LYS cc_start: 0.7824 (mttp) cc_final: 0.7352 (mtpt) REVERT: M 58 LYS cc_start: 0.6782 (mtmm) cc_final: 0.6414 (mmtt) REVERT: M 65 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7774 (t0) REVERT: K 46 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6798 (tm-30) outliers start: 40 outliers final: 31 residues processed: 167 average time/residue: 0.2166 time to fit residues: 45.5450 Evaluate side-chains 179 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 65 ASN Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 11 optimal weight: 0.0000 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN L 65 ASN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.139566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.121850 restraints weight = 8682.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.124859 restraints weight = 4346.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.126771 restraints weight = 2677.394| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5976 Z= 0.158 Angle : 0.552 8.482 8052 Z= 0.303 Chirality : 0.052 0.220 1068 Planarity : 0.002 0.019 984 Dihedral : 5.405 20.339 852 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 6.17 % Allowed : 18.17 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 50 PHE 0.011 0.002 PHE D 94 TYR 0.015 0.002 TYR M 39 Details of bonding type rmsd hydrogen bonds : bond 0.01560 ( 114) hydrogen bonds : angle 4.75302 ( 342) covalent geometry : bond 0.00328 ( 5976) covalent geometry : angle 0.55168 ( 8052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.704 Fit side-chains REVERT: A 60 LYS cc_start: 0.4540 (OUTLIER) cc_final: 0.4311 (pttm) REVERT: F 45 LYS cc_start: 0.8856 (mttt) cc_final: 0.8564 (mttp) REVERT: F 97 LYS cc_start: 0.7102 (tttt) cc_final: 0.6510 (mttm) REVERT: D 23 LYS cc_start: 0.7544 (tttt) cc_final: 0.7066 (tmtt) REVERT: E 23 LYS cc_start: 0.7902 (tttt) cc_final: 0.7297 (tmtt) REVERT: C 45 LYS cc_start: 0.8323 (mttt) cc_final: 0.7878 (mtpt) REVERT: I 58 LYS cc_start: 0.3601 (tmmt) cc_final: 0.3355 (tmmt) REVERT: I 62 GLN cc_start: 0.7988 (mt0) cc_final: 0.7725 (mt0) REVERT: M 43 LYS cc_start: 0.7809 (mttp) cc_final: 0.7304 (mtpt) REVERT: M 58 LYS cc_start: 0.6774 (mtmm) cc_final: 0.6347 (mmtt) REVERT: K 46 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6725 (tm-30) outliers start: 37 outliers final: 27 residues processed: 168 average time/residue: 0.2237 time to fit residues: 46.7592 Evaluate side-chains 174 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 0.0270 chunk 5 optimal weight: 0.0980 chunk 6 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN L 65 ASN N 65 ASN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.141661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.122609 restraints weight = 8497.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.125756 restraints weight = 4230.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.127825 restraints weight = 2626.896| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5976 Z= 0.179 Angle : 0.568 8.375 8052 Z= 0.309 Chirality : 0.052 0.209 1068 Planarity : 0.002 0.019 984 Dihedral : 5.402 23.087 852 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.54 % Rotamer: Outliers : 6.17 % Allowed : 19.50 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 PHE 0.011 0.002 PHE D 94 TYR 0.015 0.002 TYR M 39 Details of bonding type rmsd hydrogen bonds : bond 0.01693 ( 114) hydrogen bonds : angle 4.70352 ( 342) covalent geometry : bond 0.00376 ( 5976) covalent geometry : angle 0.56759 ( 8052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.727 Fit side-chains REVERT: A 60 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.4298 (pttm) REVERT: F 45 LYS cc_start: 0.8854 (mttt) cc_final: 0.8557 (mttp) REVERT: F 97 LYS cc_start: 0.6998 (tttt) cc_final: 0.6494 (mttm) REVERT: D 23 LYS cc_start: 0.7561 (tttt) cc_final: 0.7065 (tmtt) REVERT: E 23 LYS cc_start: 0.7935 (tttt) cc_final: 0.7311 (tmtt) REVERT: C 45 LYS cc_start: 0.8299 (mttt) cc_final: 0.7876 (mtpt) REVERT: I 58 LYS cc_start: 0.3616 (tmmt) cc_final: 0.3354 (tmmt) REVERT: I 62 GLN cc_start: 0.8026 (mt0) cc_final: 0.7748 (mt0) REVERT: L 43 LYS cc_start: 0.8204 (mptt) cc_final: 0.7600 (mmtp) REVERT: L 62 GLN cc_start: 0.7944 (mt0) cc_final: 0.7567 (tt0) REVERT: M 43 LYS cc_start: 0.7804 (mttp) cc_final: 0.7324 (mtpt) REVERT: M 58 LYS cc_start: 0.6988 (mtmm) cc_final: 0.6523 (mmtt) REVERT: K 46 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6701 (tm-30) outliers start: 37 outliers final: 29 residues processed: 164 average time/residue: 0.2516 time to fit residues: 51.6762 Evaluate side-chains 173 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.141288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.122380 restraints weight = 8466.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.125514 restraints weight = 4236.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.127601 restraints weight = 2625.018| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5976 Z= 0.188 Angle : 0.581 8.629 8052 Z= 0.317 Chirality : 0.052 0.253 1068 Planarity : 0.002 0.019 984 Dihedral : 5.405 20.539 852 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.35 % Favored : 92.52 % Rotamer: Outliers : 6.17 % Allowed : 19.50 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 PHE 0.012 0.002 PHE D 94 TYR 0.015 0.002 TYR M 39 Details of bonding type rmsd hydrogen bonds : bond 0.01660 ( 114) hydrogen bonds : angle 4.57811 ( 342) covalent geometry : bond 0.00394 ( 5976) covalent geometry : angle 0.58101 ( 8052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.703 Fit side-chains REVERT: F 45 LYS cc_start: 0.8826 (mttt) cc_final: 0.8523 (mttp) REVERT: F 97 LYS cc_start: 0.6950 (tttt) cc_final: 0.6402 (mttm) REVERT: D 23 LYS cc_start: 0.7571 (tttt) cc_final: 0.7059 (tmtt) REVERT: E 23 LYS cc_start: 0.7943 (tttt) cc_final: 0.7312 (tmtt) REVERT: C 45 LYS cc_start: 0.8295 (mttt) cc_final: 0.7858 (mtpt) REVERT: I 62 GLN cc_start: 0.8062 (mt0) cc_final: 0.7739 (mt0) REVERT: L 43 LYS cc_start: 0.8198 (mptt) cc_final: 0.7595 (mmtp) REVERT: M 43 LYS cc_start: 0.7797 (mttp) cc_final: 0.7309 (mtpt) REVERT: M 58 LYS cc_start: 0.6726 (mtmm) cc_final: 0.6474 (mmmt) REVERT: K 46 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6685 (tm-30) outliers start: 37 outliers final: 32 residues processed: 161 average time/residue: 0.2885 time to fit residues: 57.9657 Evaluate side-chains 175 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.138085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119325 restraints weight = 8660.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.122425 restraints weight = 4347.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.124485 restraints weight = 2689.723| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5976 Z= 0.277 Angle : 0.677 8.231 8052 Z= 0.371 Chirality : 0.052 0.193 1068 Planarity : 0.003 0.022 984 Dihedral : 6.020 24.570 852 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.56 % Favored : 89.95 % Rotamer: Outliers : 5.83 % Allowed : 19.50 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.014 0.002 PHE E 94 TYR 0.019 0.003 TYR M 39 Details of bonding type rmsd hydrogen bonds : bond 0.02228 ( 114) hydrogen bonds : angle 4.89656 ( 342) covalent geometry : bond 0.00583 ( 5976) covalent geometry : angle 0.67700 ( 8052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.75 seconds wall clock time: 42 minutes 44.21 seconds (2564.21 seconds total)