Starting phenix.real_space_refine on Fri Dec 27 15:43:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyv_27085/12_2024/8cyv_27085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyv_27085/12_2024/8cyv_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_27085/12_2024/8cyv_27085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyv_27085/12_2024/8cyv_27085.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyv_27085/12_2024/8cyv_27085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyv_27085/12_2024/8cyv_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-5532/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: 2.31, per 1000 atoms: 0.39 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: 1.52 Conformation dependent library (CDL) restraints added in 780.1 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: 0.98 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: 1.48 Time building geometry restraints manager: 1.73 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: 0.00 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: 0.110 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.640 Find NCS groups from input model: 0.210 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- 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= 0.199 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 *********************** 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 : 0.653 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: 0.2167 time to fit residues: 39.7620 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 : 0.617 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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= 0.386 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 *********************** 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 : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 LYS cc_start: 0.8195 (tttt) cc_final: 0.7756 (tmtt) REVERT: E 58 LYS cc_start: 0.7705 (tptm) cc_final: 0.6810 (mttp) REVERT: E 79 GLN cc_start: 0.8388 (mt0) cc_final: 0.7952 (mt0) REVERT: C 45 LYS cc_start: 0.8487 (mttt) cc_final: 0.8087 (mtpt) REVERT: L 46 GLU cc_start: 0.7568 (tt0) cc_final: 0.7266 (tm-30) REVERT: M 43 LYS cc_start: 0.7909 (mttp) cc_final: 0.7454 (mtpt) REVERT: M 46 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7665 (tm-30) REVERT: K 46 GLU cc_start: 0.7680 (tt0) cc_final: 0.7374 (tm-30) REVERT: J 45 LYS cc_start: 0.8372 (tttt) cc_final: 0.7369 (mttm) REVERT: J 46 GLU cc_start: 0.7840 (tt0) cc_final: 0.7242 (tm-30) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.2386 time to fit residues: 43.1889 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 : 0.680 ------------------------------------------------------------------------------- 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 42 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 6.5792 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 79 GLN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN K 65 ASN K 79 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5976 Z= 0.417 Angle : 0.662 6.705 8052 Z= 0.368 Chirality : 0.052 0.157 1068 Planarity : 0.003 0.030 984 Dihedral : 6.007 25.938 852 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.33 % Allowed : 15.50 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.37 (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 0.003 0.001 HIS A 50 PHE 0.012 0.002 PHE E 94 TYR 0.024 0.004 TYR L 39 *********************** 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 175 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: F 45 LYS cc_start: 0.8986 (mttt) cc_final: 0.8434 (mttm) REVERT: F 58 LYS cc_start: 0.7846 (tptm) cc_final: 0.7239 (mptt) REVERT: D 23 LYS cc_start: 0.7912 (tttt) cc_final: 0.7579 (tmtt) REVERT: E 23 LYS cc_start: 0.8173 (tttt) cc_final: 0.7722 (tmtt) REVERT: E 58 LYS cc_start: 0.7644 (tptm) cc_final: 0.6830 (mttp) REVERT: E 79 GLN cc_start: 0.8510 (mt0) cc_final: 0.8260 (mt0) REVERT: C 45 LYS cc_start: 0.8501 (mttt) cc_final: 0.8054 (mtpt) REVERT: L 20 GLU cc_start: 0.7220 (mp0) cc_final: 0.6971 (mp0) REVERT: L 43 LYS cc_start: 0.8347 (mptt) cc_final: 0.7949 (mmtp) REVERT: L 46 GLU cc_start: 0.7681 (tt0) cc_final: 0.7309 (tm-30) REVERT: M 43 LYS cc_start: 0.7896 (mttp) cc_final: 0.7433 (mtpt) REVERT: M 46 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7618 (tm-30) REVERT: K 46 GLU cc_start: 0.7580 (tt0) cc_final: 0.7209 (tm-30) REVERT: K 65 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8052 (t0) REVERT: J 46 GLU cc_start: 0.7815 (tt0) cc_final: 0.7526 (tm-30) outliers start: 20 outliers final: 17 residues processed: 161 average time/residue: 0.2304 time to fit residues: 45.9812 Evaluate side-chains 163 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ** C 79 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 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5976 Z= 0.461 Angle : 0.708 10.518 8052 Z= 0.393 Chirality : 0.053 0.152 1068 Planarity : 0.003 0.022 984 Dihedral : 6.322 27.945 852 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.33 % Allowed : 17.67 % Favored : 77.00 % 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: -4.58 (0.20), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.15), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 50 PHE 0.016 0.003 PHE E 94 TYR 0.024 0.004 TYR K 39 *********************** 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 183 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.825 Fit side-chains REVERT: F 45 LYS cc_start: 0.8949 (mttt) cc_final: 0.8440 (mttm) REVERT: F 58 LYS cc_start: 0.8047 (tptm) cc_final: 0.7507 (mptt) REVERT: D 23 LYS cc_start: 0.7808 (tttt) cc_final: 0.7492 (tptt) REVERT: E 23 LYS cc_start: 0.8180 (tttt) cc_final: 0.7714 (tmtt) REVERT: E 58 LYS cc_start: 0.7601 (tptm) cc_final: 0.7028 (mttp) REVERT: C 45 LYS cc_start: 0.8527 (mttt) cc_final: 0.8060 (mtpt) REVERT: I 58 LYS cc_start: 0.3864 (tmmt) cc_final: 0.3510 (tmmt) REVERT: L 46 GLU cc_start: 0.7522 (tt0) cc_final: 0.7121 (tm-30) REVERT: N 83 GLU cc_start: 0.8003 (tp30) cc_final: 0.7766 (tt0) REVERT: M 43 LYS cc_start: 0.7903 (mttp) cc_final: 0.7443 (mtpt) REVERT: K 46 GLU cc_start: 0.7645 (tt0) cc_final: 0.7122 (tm-30) REVERT: J 46 GLU cc_start: 0.7830 (tt0) cc_final: 0.7476 (tm-30) outliers start: 32 outliers final: 25 residues processed: 166 average time/residue: 0.2215 time to fit residues: 45.9902 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 : 0.592 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 VAL 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 72 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5976 Z= 0.190 Angle : 0.509 7.267 8052 Z= 0.283 Chirality : 0.051 0.194 1068 Planarity : 0.002 0.019 984 Dihedral : 5.296 21.222 852 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.33 % Allowed : 18.33 % Favored : 76.33 % 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: -4.34 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS M 50 PHE 0.010 0.002 PHE E 94 TYR 0.015 0.002 TYR M 39 *********************** 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 179 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.693 Fit side-chains REVERT: F 45 LYS cc_start: 0.8952 (mttt) cc_final: 0.8471 (mttm) REVERT: F 58 LYS cc_start: 0.7975 (tptm) cc_final: 0.7632 (mptt) REVERT: D 23 LYS cc_start: 0.7753 (tttt) cc_final: 0.7403 (tmtt) REVERT: E 23 LYS cc_start: 0.8171 (tttt) cc_final: 0.7638 (tmtt) REVERT: C 45 LYS cc_start: 0.8473 (mttt) cc_final: 0.8027 (mtpt) REVERT: I 58 LYS cc_start: 0.3561 (tmmt) cc_final: 0.3265 (tmmt) REVERT: L 46 GLU cc_start: 0.7578 (tt0) cc_final: 0.7178 (tm-30) REVERT: N 83 GLU cc_start: 0.7906 (tp30) cc_final: 0.7649 (tt0) REVERT: M 43 LYS cc_start: 0.7889 (mttp) cc_final: 0.7439 (mtpt) REVERT: M 46 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7673 (tm-30) REVERT: M 65 ASN cc_start: 0.8125 (t0) cc_final: 0.7906 (t0) REVERT: K 46 GLU cc_start: 0.7587 (tt0) cc_final: 0.7200 (tm-30) REVERT: J 46 GLU cc_start: 0.7774 (tt0) cc_final: 0.7347 (tm-30) outliers start: 32 outliers final: 22 residues processed: 160 average time/residue: 0.2258 time to fit residues: 44.9565 Evaluate side-chains 165 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 40 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 15 VAL 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 B residue 92 THR Chi-restraints excluded: chain I residue 44 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 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 27 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN L 65 ASN N 65 ASN M 62 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 5976 Z= 0.504 Angle : 0.718 7.400 8052 Z= 0.400 Chirality : 0.053 0.170 1068 Planarity : 0.003 0.019 984 Dihedral : 6.421 27.684 852 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 6.83 % Allowed : 17.33 % 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: -4.53 (0.20), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 50 PHE 0.016 0.002 PHE E 94 TYR 0.022 0.004 TYR K 39 *********************** 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 191 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.637 Fit side-chains REVERT: F 45 LYS cc_start: 0.9021 (mttt) cc_final: 0.8756 (mttp) REVERT: F 58 LYS cc_start: 0.8127 (tptm) cc_final: 0.7866 (tttp) REVERT: D 23 LYS cc_start: 0.7859 (tttt) cc_final: 0.7504 (tmtt) REVERT: E 23 LYS cc_start: 0.8179 (tttt) cc_final: 0.7635 (tmtt) REVERT: C 45 LYS cc_start: 0.8524 (mttt) cc_final: 0.8066 (mtpt) REVERT: L 46 GLU cc_start: 0.7515 (tt0) cc_final: 0.6965 (tm-30) REVERT: M 43 LYS cc_start: 0.7932 (mttp) cc_final: 0.7443 (mtpt) REVERT: K 46 GLU cc_start: 0.7666 (tt0) cc_final: 0.7090 (tm-30) REVERT: J 46 GLU cc_start: 0.7829 (tt0) cc_final: 0.7312 (tm-30) outliers start: 41 outliers final: 32 residues processed: 170 average time/residue: 0.2283 time to fit residues: 48.0507 Evaluate side-chains 177 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 D residue 92 THR 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 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 44 THR Chi-restraints excluded: chain I residue 52 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 62 GLN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5976 Z= 0.290 Angle : 0.585 7.906 8052 Z= 0.325 Chirality : 0.052 0.203 1068 Planarity : 0.002 0.019 984 Dihedral : 5.766 22.963 852 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 6.50 % Allowed : 18.67 % Favored : 74.83 % 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: -4.32 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 50 PHE 0.013 0.002 PHE E 94 TYR 0.016 0.003 TYR M 39 *********************** 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 189 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: F 45 LYS cc_start: 0.9002 (mttt) cc_final: 0.8743 (mttp) REVERT: F 58 LYS cc_start: 0.8045 (tptm) cc_final: 0.7610 (mptt) REVERT: D 23 LYS cc_start: 0.7809 (tttt) cc_final: 0.7404 (tmtt) REVERT: E 23 LYS cc_start: 0.8069 (tttt) cc_final: 0.7537 (tmtt) REVERT: C 45 LYS cc_start: 0.8486 (mttt) cc_final: 0.8052 (mtpt) REVERT: I 62 GLN cc_start: 0.8022 (mt0) cc_final: 0.7747 (mt0) REVERT: L 46 GLU cc_start: 0.7549 (tt0) cc_final: 0.7085 (tm-30) REVERT: M 43 LYS cc_start: 0.7915 (mttp) cc_final: 0.7456 (mtpt) REVERT: K 46 GLU cc_start: 0.7613 (tt0) cc_final: 0.7088 (tm-30) REVERT: J 46 GLU cc_start: 0.7772 (tt0) cc_final: 0.7300 (tm-30) outliers start: 39 outliers final: 31 residues processed: 171 average time/residue: 0.2119 time to fit residues: 45.4647 Evaluate side-chains 180 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 62 GLN M 65 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5366 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= 0.424 Angle : 0.681 7.747 8052 Z= 0.378 Chirality : 0.053 0.178 1068 Planarity : 0.003 0.020 984 Dihedral : 6.255 26.282 852 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.78 % Favored : 89.09 % Rotamer: Outliers : 6.67 % Allowed : 19.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.34 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.015 0.002 PHE D 94 TYR 0.020 0.003 TYR K 39 *********************** 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 188 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.675 Fit side-chains REVERT: F 45 LYS cc_start: 0.9003 (mttt) cc_final: 0.8697 (mttp) REVERT: D 23 LYS cc_start: 0.7733 (tttt) cc_final: 0.7355 (tmtt) REVERT: D 65 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7170 (t0) REVERT: E 23 LYS cc_start: 0.8019 (tttt) cc_final: 0.7521 (tmtt) REVERT: E 24 GLN cc_start: 0.4953 (OUTLIER) cc_final: 0.4597 (mt0) REVERT: C 38 LEU cc_start: 0.8720 (mp) cc_final: 0.8501 (mt) REVERT: C 45 LYS cc_start: 0.8505 (mttt) cc_final: 0.8066 (mtpt) REVERT: L 46 GLU cc_start: 0.7449 (tt0) cc_final: 0.7018 (tm-30) REVERT: M 43 LYS cc_start: 0.7909 (mttp) cc_final: 0.7456 (mtpt) REVERT: K 46 GLU cc_start: 0.7662 (tt0) cc_final: 0.7061 (tm-30) REVERT: J 46 GLU cc_start: 0.7712 (tt0) cc_final: 0.7321 (tm-30) outliers start: 40 outliers final: 30 residues processed: 170 average time/residue: 0.2208 time to fit residues: 46.7396 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 : 0.596 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 24 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5368 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= 0.348 Angle : 0.644 8.426 8052 Z= 0.356 Chirality : 0.053 0.207 1068 Planarity : 0.002 0.019 984 Dihedral : 6.032 23.269 852 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.82 % Favored : 90.93 % Rotamer: Outliers : 6.67 % Allowed : 19.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.27 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.16), 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 0.017 0.003 TYR L 39 *********************** 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 192 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.667 Fit side-chains REVERT: A 60 LYS cc_start: 0.4566 (OUTLIER) cc_final: 0.4341 (pttm) REVERT: F 45 LYS cc_start: 0.8992 (mttt) cc_final: 0.8752 (mttp) REVERT: D 23 LYS cc_start: 0.7707 (tttt) cc_final: 0.7336 (tmtt) REVERT: E 23 LYS cc_start: 0.8000 (tttt) cc_final: 0.7481 (tmtt) REVERT: E 24 GLN cc_start: 0.5014 (OUTLIER) cc_final: 0.4646 (mt0) REVERT: C 38 LEU cc_start: 0.8691 (mp) cc_final: 0.8477 (mt) REVERT: C 45 LYS cc_start: 0.8517 (mttt) cc_final: 0.8068 (mtpt) REVERT: I 62 GLN cc_start: 0.7841 (mt0) cc_final: 0.7625 (mt0) REVERT: L 46 GLU cc_start: 0.7472 (tt0) cc_final: 0.7060 (tm-30) REVERT: N 94 PHE cc_start: 0.7620 (t80) cc_final: 0.7217 (t80) REVERT: M 43 LYS cc_start: 0.7936 (mttp) cc_final: 0.7485 (mtpt) REVERT: M 46 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7777 (tm-30) REVERT: K 46 GLU cc_start: 0.7597 (tt0) cc_final: 0.7040 (tm-30) REVERT: J 46 GLU cc_start: 0.7685 (tt0) cc_final: 0.7188 (tm-30) outliers start: 40 outliers final: 32 residues processed: 171 average time/residue: 0.2210 time to fit residues: 47.0893 Evaluate side-chains 183 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 24 GLN 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 65 ASN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 5976 Z= 0.457 Angle : 0.730 7.998 8052 Z= 0.403 Chirality : 0.054 0.181 1068 Planarity : 0.003 0.020 984 Dihedral : 6.429 25.811 852 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.27 % Favored : 88.24 % Rotamer: Outliers : 6.50 % Allowed : 19.67 % Favored : 73.83 % 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: -4.37 (0.21), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.017 0.002 PHE D 94 TYR 0.022 0.004 TYR K 39 ********************** 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 188 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.587 Fit side-chains REVERT: F 45 LYS cc_start: 0.9001 (mttt) cc_final: 0.8707 (mttp) REVERT: D 23 LYS cc_start: 0.7747 (tttt) cc_final: 0.7377 (tmtt) REVERT: D 65 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7196 (t0) REVERT: E 23 LYS cc_start: 0.8004 (tttt) cc_final: 0.7497 (tmtt) REVERT: C 38 LEU cc_start: 0.8694 (mp) cc_final: 0.8486 (mt) REVERT: C 45 LYS cc_start: 0.8507 (mttt) cc_final: 0.8067 (mtpt) REVERT: L 46 GLU cc_start: 0.7443 (tt0) cc_final: 0.6958 (tm-30) REVERT: N 94 PHE cc_start: 0.7682 (t80) cc_final: 0.7268 (t80) REVERT: M 43 LYS cc_start: 0.7956 (mttp) cc_final: 0.7488 (mtpt) REVERT: K 46 GLU cc_start: 0.7710 (tt0) cc_final: 0.7199 (tm-30) REVERT: J 46 GLU cc_start: 0.7642 (tt0) cc_final: 0.7284 (tm-30) outliers start: 39 outliers final: 31 residues processed: 169 average time/residue: 0.2105 time to fit residues: 44.4381 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 : 0.650 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain D residue 72 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN I 62 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN N 65 ASN M 65 ASN M 79 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.143361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.124258 restraints weight = 8163.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.127617 restraints weight = 4086.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.129794 restraints weight = 2494.234| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5976 Z= 0.162 Angle : 0.553 8.677 8052 Z= 0.304 Chirality : 0.052 0.220 1068 Planarity : 0.002 0.021 984 Dihedral : 5.371 20.411 852 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.64 % Favored : 93.87 % Rotamer: Outliers : 4.00 % Allowed : 21.83 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.03 (0.22), residues: 816 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.011 0.002 PHE E 94 TYR 0.013 0.001 TYR M 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.51 seconds wall clock time: 26 minutes 34.96 seconds (1594.96 seconds total)