Starting phenix.real_space_refine on Fri Aug 22 13:10:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.map" model { file = "/net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jey_36203/08_2025/8jey_36203.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1914 2.51 5 N 528 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Time building chain proxies: 0.77, per 1000 atoms: 0.25 Number of scatterers: 3060 At special positions: 0 Unit cell: (75.53, 107.07, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 606 8.00 N 528 7.00 C 1914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 75.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.215A pdb=" N VAL A 3 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS B 6 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET A 5 " --> pdb=" O LYS B 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.523A pdb=" N ALA A 11 " --> pdb=" O LYS C 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 16 removed outlier: 6.701A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 29 removed outlier: 9.036A pdb=" N LYS A 23 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL B 26 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 25 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU B 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 27 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN A 24 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY C 25 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 40 removed outlier: 6.924A pdb=" N GLY B 36 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR C 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.586A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52 removed outlier: 5.995A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 66 removed outlier: 8.676A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N THR B 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LYS A 58 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU B 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL B 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 59 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS C 60 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 61 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.490A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.215A pdb=" N VAL D 3 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS E 6 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET D 5 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.524A pdb=" N ALA D 11 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 16 removed outlier: 6.701A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 23 through 29 removed outlier: 9.034A pdb=" N LYS D 23 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL E 26 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY D 25 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLU E 28 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA D 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN D 24 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY F 25 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40 removed outlier: 6.924A pdb=" N GLY E 36 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR F 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.586A pdb=" N LYS D 43 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 49 through 52 removed outlier: 5.994A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 55 through 66 removed outlier: 8.675A pdb=" N ALA D 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N THR E 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LYS D 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU E 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL E 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU D 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS F 58 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR D 59 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS F 60 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU D 61 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.490A pdb=" N ALA D 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 46 hydrogen bonds defined for protein. 138 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: 0.27 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 335 1.46 - 1.57: 1711 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 3072 Sorted by residual: bond pdb=" N VAL A 26 " pdb=" CA VAL A 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.48e+00 bond pdb=" N VAL E 26 " pdb=" CA VAL E 26 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.06e+00 bond pdb=" N VAL D 26 " pdb=" CA VAL D 26 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.06e+00 bond pdb=" N VAL C 26 " pdb=" CA VAL C 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.89e+00 bond pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 ... (remaining 3067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 3573 0.97 - 1.94: 403 1.94 - 2.91: 92 2.91 - 3.88: 24 3.88 - 4.84: 18 Bond angle restraints: 4110 Sorted by residual: angle pdb=" N GLU E 13 " pdb=" CA GLU E 13 " pdb=" C GLU E 13 " ideal model delta sigma weight residual 112.58 108.44 4.14 1.22e+00 6.72e-01 1.15e+01 angle pdb=" N GLU D 13 " pdb=" CA GLU D 13 " pdb=" C GLU D 13 " ideal model delta sigma weight residual 112.58 108.45 4.13 1.22e+00 6.72e-01 1.15e+01 angle pdb=" N GLU B 13 " pdb=" CA GLU B 13 " pdb=" C GLU B 13 " ideal model delta sigma weight residual 112.58 108.46 4.12 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N GLU A 13 " pdb=" CA GLU A 13 " pdb=" C GLU A 13 " ideal model delta sigma weight residual 112.58 108.47 4.11 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N GLU F 13 " pdb=" CA GLU F 13 " pdb=" C GLU F 13 " ideal model delta sigma weight residual 112.58 108.51 4.07 1.22e+00 6.72e-01 1.11e+01 ... (remaining 4105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.63: 1508 9.63 - 19.26: 244 19.26 - 28.89: 60 28.89 - 38.52: 36 38.52 - 48.15: 12 Dihedral angle restraints: 1860 sinusoidal: 684 harmonic: 1176 Sorted by residual: dihedral pdb=" CA LYS C 58 " pdb=" C LYS C 58 " pdb=" N THR C 59 " pdb=" CA THR C 59 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LYS F 58 " pdb=" C LYS F 58 " pdb=" N THR F 59 " pdb=" CA THR F 59 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LYS D 58 " pdb=" C LYS D 58 " pdb=" N THR D 59 " pdb=" CA THR D 59 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 315 0.038 - 0.076: 82 0.076 - 0.114: 93 0.114 - 0.152: 11 0.152 - 0.190: 9 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA GLU D 20 " pdb=" N GLU D 20 " pdb=" C GLU D 20 " pdb=" CB GLU D 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA GLU E 20 " pdb=" N GLU E 20 " pdb=" C GLU E 20 " pdb=" CB GLU E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA GLU A 20 " pdb=" N GLU A 20 " pdb=" C GLU A 20 " pdb=" CB GLU A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 507 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 8 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU F 8 " -0.017 2.00e-02 2.50e+03 pdb=" O LEU F 8 " 0.006 2.00e-02 2.50e+03 pdb=" N SER F 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 8 " -0.005 2.00e-02 2.50e+03 9.97e-03 9.94e-01 pdb=" C LEU C 8 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU C 8 " -0.006 2.00e-02 2.50e+03 pdb=" N SER C 9 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 8 " -0.005 2.00e-02 2.50e+03 9.73e-03 9.48e-01 pdb=" C LEU A 8 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 8 " -0.006 2.00e-02 2.50e+03 pdb=" N SER A 9 " -0.006 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 935 2.85 - 3.36: 2546 3.36 - 3.88: 4675 3.88 - 4.39: 4989 4.39 - 4.90: 10500 Nonbonded interactions: 23645 Sorted by model distance: nonbonded pdb=" NZ LYS B 6 " pdb=" OE2 GLU B 20 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYS F 6 " pdb=" OE2 GLU F 20 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYS E 6 " pdb=" OE2 GLU E 20 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS A 6 " pdb=" OE2 GLU A 20 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS C 6 " pdb=" OE2 GLU C 20 " model vdw 2.340 3.120 ... (remaining 23640 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 2.910 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.004 0.035 3072 Z= 0.264 Angle : 0.746 4.845 4110 Z= 0.464 Chirality : 0.058 0.190 510 Planarity : 0.002 0.010 510 Dihedral : 11.672 48.153 1116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.60 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.007 0.002 PHE E 4 HIS 0.001 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3072) covalent geometry : angle 0.74567 ( 4110) hydrogen bonds : bond 0.18691 ( 46) hydrogen bonds : angle 8.65688 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.5000 time to fit residues: 29.1814 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.171830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.157351 restraints weight = 3431.002| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.68 r_work: 0.4166 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3072 Z= 0.151 Angle : 0.518 4.948 4110 Z= 0.288 Chirality : 0.050 0.128 510 Planarity : 0.002 0.007 510 Dihedral : 5.012 16.942 432 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.53 % Allowed : 8.01 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR D 39 PHE 0.005 0.001 PHE F 4 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3072) covalent geometry : angle 0.51778 ( 4110) hydrogen bonds : bond 0.02957 ( 46) hydrogen bonds : angle 5.84758 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.086 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 55 average time/residue: 0.4756 time to fit residues: 26.9038 Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.165273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151190 restraints weight = 3484.714| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 1.69 r_work: 0.4101 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 3072 Z= 0.314 Angle : 0.646 4.819 4110 Z= 0.365 Chirality : 0.053 0.138 510 Planarity : 0.003 0.011 510 Dihedral : 6.329 18.421 432 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.24 % Allowed : 11.22 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.005 TYR F 39 PHE 0.008 0.004 PHE F 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 3072) covalent geometry : angle 0.64563 ( 4110) hydrogen bonds : bond 0.03362 ( 46) hydrogen bonds : angle 5.71645 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.074 Fit side-chains REVERT: C 5 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7235 (ttt) REVERT: E 5 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7595 (ttt) outliers start: 7 outliers final: 0 residues processed: 58 average time/residue: 0.5406 time to fit residues: 32.0717 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain E residue 5 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.167346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.154312 restraints weight = 3458.042| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 1.57 r_work: 0.4136 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3072 Z= 0.180 Angle : 0.530 4.895 4110 Z= 0.292 Chirality : 0.051 0.126 510 Planarity : 0.002 0.006 510 Dihedral : 5.778 17.881 432 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.85 % Allowed : 11.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR D 39 PHE 0.004 0.002 PHE F 4 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 3072) covalent geometry : angle 0.52987 ( 4110) hydrogen bonds : bond 0.02337 ( 46) hydrogen bonds : angle 5.51620 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.126 Fit side-chains REVERT: A 28 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6775 (tm-30) outliers start: 12 outliers final: 4 residues processed: 60 average time/residue: 0.4744 time to fit residues: 29.2278 Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.165535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.152686 restraints weight = 3460.665| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.56 r_work: 0.4123 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 3072 Z= 0.218 Angle : 0.561 4.536 4110 Z= 0.309 Chirality : 0.051 0.126 510 Planarity : 0.002 0.008 510 Dihedral : 5.898 18.279 432 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.85 % Allowed : 11.54 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR D 39 PHE 0.006 0.002 PHE F 4 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 3072) covalent geometry : angle 0.56107 ( 4110) hydrogen bonds : bond 0.02431 ( 46) hydrogen bonds : angle 5.45697 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.126 Fit side-chains REVERT: C 5 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7375 (ttt) REVERT: E 5 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7507 (ttt) outliers start: 12 outliers final: 2 residues processed: 61 average time/residue: 0.4647 time to fit residues: 29.1249 Evaluate side-chains 63 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 5 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.0000 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.157504 restraints weight = 3505.984| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.64 r_work: 0.4174 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3072 Z= 0.106 Angle : 0.492 6.212 4110 Z= 0.259 Chirality : 0.051 0.122 510 Planarity : 0.001 0.007 510 Dihedral : 5.269 17.335 432 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.81 % Allowed : 11.54 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 PHE 0.002 0.001 PHE F 4 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3072) covalent geometry : angle 0.49248 ( 4110) hydrogen bonds : bond 0.01770 ( 46) hydrogen bonds : angle 5.18937 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.096 Fit side-chains REVERT: A 5 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7383 (ttt) REVERT: C 5 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7273 (ttt) REVERT: C 46 GLU cc_start: 0.7813 (tt0) cc_final: 0.7445 (tt0) outliers start: 15 outliers final: 2 residues processed: 63 average time/residue: 0.4117 time to fit residues: 26.6326 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.164722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.151735 restraints weight = 3470.768| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.58 r_work: 0.4117 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3072 Z= 0.260 Angle : 0.603 6.878 4110 Z= 0.328 Chirality : 0.052 0.170 510 Planarity : 0.003 0.009 510 Dihedral : 5.883 18.975 432 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.88 % Allowed : 13.46 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR F 39 PHE 0.008 0.003 PHE F 4 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 3072) covalent geometry : angle 0.60252 ( 4110) hydrogen bonds : bond 0.02512 ( 46) hydrogen bonds : angle 5.41291 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.072 Fit side-chains REVERT: B 5 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7670 (ttt) REVERT: C 5 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7442 (ttt) REVERT: C 46 GLU cc_start: 0.7726 (tt0) cc_final: 0.7376 (tt0) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.4329 time to fit residues: 27.0799 Evaluate side-chains 66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.169392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.155806 restraints weight = 3626.353| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 1.68 r_work: 0.4155 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3072 Z= 0.143 Angle : 0.535 7.046 4110 Z= 0.278 Chirality : 0.051 0.141 510 Planarity : 0.002 0.011 510 Dihedral : 5.473 18.114 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR D 39 PHE 0.004 0.001 PHE F 4 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3072) covalent geometry : angle 0.53465 ( 4110) hydrogen bonds : bond 0.01922 ( 46) hydrogen bonds : angle 5.23672 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.069 Fit side-chains REVERT: C 5 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7371 (ttt) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.4167 time to fit residues: 25.7523 Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 0.0040 chunk 0 optimal weight: 7.9990 overall best weight: 2.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.166453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.153250 restraints weight = 3543.236| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.59 r_work: 0.4143 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3072 Z= 0.217 Angle : 0.589 8.053 4110 Z= 0.310 Chirality : 0.052 0.160 510 Planarity : 0.002 0.013 510 Dihedral : 5.741 18.634 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR D 39 PHE 0.007 0.002 PHE F 4 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 3072) covalent geometry : angle 0.58885 ( 4110) hydrogen bonds : bond 0.02270 ( 46) hydrogen bonds : angle 5.33766 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.150 Fit side-chains REVERT: B 5 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7626 (ttt) REVERT: C 5 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7404 (ttt) REVERT: C 46 GLU cc_start: 0.7749 (tt0) cc_final: 0.7412 (tt0) REVERT: E 5 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7518 (ttt) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.4261 time to fit residues: 26.6837 Evaluate side-chains 67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.167852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.154911 restraints weight = 3384.286| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.54 r_work: 0.4156 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3072 Z= 0.178 Angle : 0.577 8.765 4110 Z= 0.297 Chirality : 0.052 0.161 510 Planarity : 0.002 0.014 510 Dihedral : 5.601 18.366 432 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 15.06 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR F 39 PHE 0.005 0.002 PHE F 4 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3072) covalent geometry : angle 0.57725 ( 4110) hydrogen bonds : bond 0.02114 ( 46) hydrogen bonds : angle 5.29057 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.112 Fit side-chains REVERT: B 5 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7602 (ttt) REVERT: C 5 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7373 (ttt) REVERT: C 46 GLU cc_start: 0.7721 (tt0) cc_final: 0.7395 (tt0) REVERT: E 5 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7519 (ttt) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.4903 time to fit residues: 30.6190 Evaluate side-chains 67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.165417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.152188 restraints weight = 3517.722| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.61 r_work: 0.4133 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 3072 Z= 0.273 Angle : 0.640 7.807 4110 Z= 0.340 Chirality : 0.054 0.178 510 Planarity : 0.003 0.014 510 Dihedral : 6.019 19.241 432 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.56 % Allowed : 15.06 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.004 TYR F 39 PHE 0.009 0.003 PHE F 4 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 3072) covalent geometry : angle 0.64000 ( 4110) hydrogen bonds : bond 0.02563 ( 46) hydrogen bonds : angle 5.47915 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1152.82 seconds wall clock time: 20 minutes 24.55 seconds (1224.55 seconds total)