Starting phenix.real_space_refine on Mon Apr 28 17:43:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.map" model { file = "/net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h6b_0148/04_2025/6h6b_0148.cif" } resolution = 3.4 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= 0.002 sd= 0.007 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 C 2480 2.51 5 N 680 2.21 5 O 800 1.98 5 H 4100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 4.00, per 1000 atoms: 0.50 Number of scatterers: 8060 At special positions: 0 Unit cell: (92.241, 90.579, 42.381, 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) O 800 8.00 N 680 7.00 C 2480 6.00 H 4100 1.00 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: 1.79 Conformation dependent library (CDL) restraints added in 665.9 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 980 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 56 removed outlier: 6.981A pdb=" N VAL B 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS B 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY C 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS A 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY B 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY A 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N HIS H 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL A 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N VAL H 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY A 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR H 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA A 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA H 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL G 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL H 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS G 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY H 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.255A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL H 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN G 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.566A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 74 through 77 removed outlier: 6.890A pdb=" N VAL B 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL H 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA A 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL G 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 88 through 92 removed outlier: 6.965A pdb=" N ALA C 90 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR C 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 90 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE A 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA H 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ALA A 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA H 90 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR H 92 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 46 through 56 removed outlier: 6.968A pdb=" N VAL D 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL F 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY F 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N HIS E 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR E 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA E 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY E 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 10.224A pdb=" N HIS J 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL E 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL J 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY E 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR J 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA J 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL I 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL J 49 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS I 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY J 51 " --> pdb=" O HIS I 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.215A pdb=" N VAL D 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL F 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 70 through 71 removed outlier: 6.590A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.887A pdb=" N VAL D 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL J 77 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA E 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL I 77 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 88 through 92 removed outlier: 6.945A pdb=" N ALA F 90 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA D 91 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR F 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ILE E 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA J 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N ALA E 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA J 90 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA I 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR J 92 " --> pdb=" O ALA I 91 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 2.33 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 4100 0.98 - 1.13: 0 1.13 - 1.27: 690 1.27 - 1.42: 800 1.42 - 1.57: 2490 Bond restraints: 8080 Sorted by residual: bond pdb=" CB VAL D 70 " pdb=" CG2 VAL D 70 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB VAL I 70 " pdb=" CG2 VAL I 70 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB VAL J 70 " pdb=" CG2 VAL J 70 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB VAL C 70 " pdb=" CG2 VAL C 70 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB VAL H 70 " pdb=" CG2 VAL H 70 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 8075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 14588 4.98 - 9.95: 32 9.95 - 14.93: 10 14.93 - 19.91: 0 19.91 - 24.88: 30 Bond angle restraints: 14660 Sorted by residual: angle pdb=" CG2 VAL F 95 " pdb=" CB VAL F 95 " pdb=" HB VAL F 95 " ideal model delta sigma weight residual 108.00 83.12 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" CG2 VAL D 95 " pdb=" CB VAL D 95 " pdb=" HB VAL D 95 " ideal model delta sigma weight residual 108.00 83.12 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" CG2 VAL J 95 " pdb=" CB VAL J 95 " pdb=" HB VAL J 95 " ideal model delta sigma weight residual 108.00 83.18 24.82 3.00e+00 1.11e-01 6.84e+01 angle pdb=" CG2 VAL A 95 " pdb=" CB VAL A 95 " pdb=" HB VAL A 95 " ideal model delta sigma weight residual 108.00 83.19 24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" CG2 VAL C 95 " pdb=" CB VAL C 95 " pdb=" HB VAL C 95 " ideal model delta sigma weight residual 108.00 83.19 24.81 3.00e+00 1.11e-01 6.84e+01 ... (remaining 14655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.90: 3332 11.90 - 23.81: 168 23.81 - 35.71: 70 35.71 - 47.61: 80 47.61 - 59.51: 60 Dihedral angle restraints: 3710 sinusoidal: 2030 harmonic: 1680 Sorted by residual: dihedral pdb=" CA PHE B 94 " pdb=" C PHE B 94 " pdb=" N VAL B 95 " pdb=" CA VAL B 95 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A 94 " pdb=" C PHE A 94 " pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE I 94 " pdb=" C PHE I 94 " pdb=" N VAL I 95 " pdb=" CA VAL I 95 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 3707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 710 0.321 - 0.642: 0 0.642 - 0.963: 0 0.963 - 1.284: 0 1.284 - 1.605: 10 Chirality restraints: 720 Sorted by residual: chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CB VAL J 95 " pdb=" CA VAL J 95 " pdb=" CG1 VAL J 95 " pdb=" CG2 VAL J 95 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.60 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.60 2.00e-01 2.50e+01 6.44e+01 ... (remaining 717 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 76 " -0.006 2.00e-02 2.50e+03 1.07e-02 1.14e+00 pdb=" N VAL A 77 " 0.018 2.00e-02 2.50e+03 pdb=" CA VAL A 77 " -0.005 2.00e-02 2.50e+03 pdb=" H VAL A 77 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.010 2.00e-02 2.50e+03 6.90e-03 1.07e+00 pdb=" CG HIS B 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS B 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 50 " -0.010 2.00e-02 2.50e+03 6.87e-03 1.06e+00 pdb=" CG HIS I 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS I 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS I 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS I 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS I 50 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS I 50 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS I 50 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS I 50 " -0.004 2.00e-02 2.50e+03 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.30: 1609 2.30 - 2.85: 18158 2.85 - 3.40: 16698 3.40 - 3.95: 25141 3.95 - 4.50: 36108 Nonbonded interactions: 97714 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" HZ1 LYS E 80 " model vdw 1.753 2.450 nonbonded pdb=" HB VAL B 95 " pdb="HG13 VAL B 95 " model vdw 1.764 1.952 nonbonded pdb=" HB VAL D 95 " pdb="HG13 VAL D 95 " model vdw 1.764 1.952 nonbonded pdb=" HB VAL C 95 " pdb="HG13 VAL C 95 " model vdw 1.766 1.952 nonbonded pdb=" HB VAL A 95 " pdb="HG13 VAL A 95 " model vdw 1.766 1.952 ... (remaining 97709 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 1.600 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: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.008 0.045 3980 Z= 0.325 Angle : 1.101 10.230 5400 Z= 0.604 Chirality : 0.198 1.605 720 Planarity : 0.002 0.008 670 Dihedral : 8.131 35.210 1310 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -4.80 (0.21), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS G 50 PHE 0.007 0.003 PHE D 94 TYR 0.002 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.24005 ( 60) hydrogen bonds : angle 9.01586 ( 180) covalent geometry : bond 0.00762 ( 3980) covalent geometry : angle 1.10061 ( 5400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 THR cc_start: 0.6415 (m) cc_final: 0.6205 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1830 time to fit residues: 21.1233 Evaluate side-chains 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.223880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.193435 restraints weight = 13910.695| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 2.84 r_work: 0.4585 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3980 Z= 0.118 Angle : 0.810 11.064 5400 Z= 0.437 Chirality : 0.182 1.562 720 Planarity : 0.002 0.009 670 Dihedral : 5.715 16.871 580 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.25 % Allowed : 6.75 % Favored : 93.00 % 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: -4.21 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.18), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.015 0.002 PHE D 94 TYR 0.004 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02528 ( 60) hydrogen bonds : angle 4.67274 ( 180) covalent geometry : bond 0.00299 ( 3980) covalent geometry : angle 0.81001 ( 5400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6876 (mm-30) REVERT: G 65 ASN cc_start: 0.7560 (t0) cc_final: 0.7183 (t0) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1737 time to fit residues: 14.3746 Evaluate side-chains 44 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.211010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.181326 restraints weight = 13899.964| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 3.05 r_work: 0.4440 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3980 Z= 0.216 Angle : 0.902 11.345 5400 Z= 0.491 Chirality : 0.189 1.614 720 Planarity : 0.002 0.008 670 Dihedral : 6.500 19.373 580 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.61 % Favored : 83.39 % Rotamer: Outliers : 1.25 % Allowed : 8.00 % Favored : 90.75 % 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: -3.94 (0.25), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS I 50 PHE 0.013 0.003 PHE A 94 TYR 0.002 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 60) hydrogen bonds : angle 4.32120 ( 180) covalent geometry : bond 0.00475 ( 3980) covalent geometry : angle 0.90195 ( 5400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.620 Fit side-chains REVERT: B 83 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7121 (mm-30) REVERT: D 46 GLU cc_start: 0.7371 (mp0) cc_final: 0.7063 (mp0) REVERT: I 46 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7493 (mt-10) REVERT: J 46 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7007 (mm-30) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.1755 time to fit residues: 14.7216 Evaluate side-chains 46 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.213057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.183682 restraints weight = 13999.350| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 2.92 r_work: 0.4441 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3980 Z= 0.184 Angle : 0.853 11.041 5400 Z= 0.462 Chirality : 0.183 1.567 720 Planarity : 0.002 0.008 670 Dihedral : 6.064 18.993 580 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % Rotamer: Outliers : 4.75 % Allowed : 9.00 % Favored : 86.25 % 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: -3.79 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 50 PHE 0.010 0.002 PHE D 94 TYR 0.002 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02466 ( 60) hydrogen bonds : angle 4.03273 ( 180) covalent geometry : bond 0.00406 ( 3980) covalent geometry : angle 0.85338 ( 5400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.633 Fit side-chains REVERT: B 83 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7134 (mm-30) REVERT: I 46 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7450 (mt-10) REVERT: J 46 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: J 83 GLU cc_start: 0.7365 (mp0) cc_final: 0.6954 (mp0) outliers start: 19 outliers final: 15 residues processed: 56 average time/residue: 0.1778 time to fit residues: 14.9336 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4820 r_free = 0.4820 target = 0.212712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183280 restraints weight = 13577.673| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 3.04 r_work: 0.4460 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3980 Z= 0.130 Angle : 0.796 11.163 5400 Z= 0.428 Chirality : 0.183 1.558 720 Planarity : 0.001 0.005 670 Dihedral : 5.556 16.996 580 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 2.75 % Allowed : 12.00 % Favored : 85.25 % 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: -3.63 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.011 0.002 PHE J 94 TYR 0.002 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02147 ( 60) hydrogen bonds : angle 3.92495 ( 180) covalent geometry : bond 0.00304 ( 3980) covalent geometry : angle 0.79566 ( 5400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.561 Fit side-chains REVERT: B 83 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6905 (mm-30) REVERT: G 75 THR cc_start: 0.7306 (m) cc_final: 0.7098 (t) REVERT: H 57 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7580 (tp30) REVERT: I 46 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7492 (mt-10) REVERT: J 46 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6955 (mm-30) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1821 time to fit residues: 15.2150 Evaluate side-chains 61 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4772 r_free = 0.4772 target = 0.209039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.179623 restraints weight = 13934.434| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 3.08 r_work: 0.4404 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3980 Z= 0.208 Angle : 0.861 11.084 5400 Z= 0.468 Chirality : 0.184 1.576 720 Planarity : 0.002 0.006 670 Dihedral : 5.971 18.234 580 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.18 % Favored : 79.82 % Rotamer: Outliers : 4.50 % Allowed : 11.25 % Favored : 84.25 % 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: -3.73 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 50 PHE 0.010 0.002 PHE J 94 TYR 0.003 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02605 ( 60) hydrogen bonds : angle 4.20894 ( 180) covalent geometry : bond 0.00450 ( 3980) covalent geometry : angle 0.86084 ( 5400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.566 Fit side-chains REVERT: H 83 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6800 (mm-30) REVERT: I 46 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7567 (mt-10) REVERT: J 46 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: J 83 GLU cc_start: 0.7410 (mp0) cc_final: 0.6994 (mp0) outliers start: 18 outliers final: 17 residues processed: 55 average time/residue: 0.1782 time to fit residues: 14.6440 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.209362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.180650 restraints weight = 13986.018| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.98 r_work: 0.4409 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3980 Z= 0.196 Angle : 0.849 11.012 5400 Z= 0.461 Chirality : 0.184 1.566 720 Planarity : 0.002 0.009 670 Dihedral : 5.942 17.386 580 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 4.75 % Allowed : 10.50 % Favored : 84.75 % 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: -3.83 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.013 0.002 PHE C 94 TYR 0.004 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 60) hydrogen bonds : angle 4.20975 ( 180) covalent geometry : bond 0.00422 ( 3980) covalent geometry : angle 0.84950 ( 5400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.635 Fit side-chains REVERT: H 57 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7562 (tp30) REVERT: H 83 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6824 (mm-30) REVERT: I 46 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7595 (mt-10) REVERT: J 46 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: J 83 GLU cc_start: 0.7512 (mp0) cc_final: 0.7144 (mp0) outliers start: 19 outliers final: 18 residues processed: 55 average time/residue: 0.1785 time to fit residues: 14.9090 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 0.0570 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.211574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.182886 restraints weight = 13973.324| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.99 r_work: 0.4439 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3980 Z= 0.151 Angle : 0.810 11.057 5400 Z= 0.437 Chirality : 0.183 1.555 720 Planarity : 0.002 0.009 670 Dihedral : 5.577 16.281 580 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Rotamer: Outliers : 4.50 % Allowed : 11.25 % Favored : 84.25 % 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: -3.85 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 50 PHE 0.020 0.002 PHE C 94 TYR 0.003 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02165 ( 60) hydrogen bonds : angle 4.08337 ( 180) covalent geometry : bond 0.00339 ( 3980) covalent geometry : angle 0.80960 ( 5400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.726 Fit side-chains REVERT: H 57 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7529 (tp30) REVERT: H 83 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6866 (mm-30) REVERT: I 46 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7513 (mt-10) REVERT: J 46 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6966 (mm-30) REVERT: J 83 GLU cc_start: 0.7507 (mp0) cc_final: 0.7143 (mp0) outliers start: 18 outliers final: 17 residues processed: 55 average time/residue: 0.1834 time to fit residues: 15.4437 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4816 r_free = 0.4816 target = 0.212351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.183169 restraints weight = 13984.156| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 3.03 r_work: 0.4443 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3980 Z= 0.144 Angle : 0.798 11.049 5400 Z= 0.430 Chirality : 0.184 1.556 720 Planarity : 0.002 0.008 670 Dihedral : 5.429 16.019 580 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.61 % Favored : 83.39 % Rotamer: Outliers : 4.50 % Allowed : 11.25 % Favored : 84.25 % 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: -3.78 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.014 0.002 PHE J 94 TYR 0.003 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02143 ( 60) hydrogen bonds : angle 4.05071 ( 180) covalent geometry : bond 0.00326 ( 3980) covalent geometry : angle 0.79825 ( 5400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.616 Fit side-chains REVERT: A 66 VAL cc_start: 0.8307 (t) cc_final: 0.7870 (m) REVERT: H 57 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7537 (tp30) REVERT: H 83 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6875 (mm-30) REVERT: I 46 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7562 (mt-10) REVERT: J 46 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: J 83 GLU cc_start: 0.7564 (mp0) cc_final: 0.7188 (mp0) outliers start: 18 outliers final: 16 residues processed: 57 average time/residue: 0.1832 time to fit residues: 15.6641 Evaluate side-chains 60 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4833 r_free = 0.4833 target = 0.213524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.183529 restraints weight = 13734.574| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 3.00 r_work: 0.4456 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3980 Z= 0.132 Angle : 0.788 11.077 5400 Z= 0.423 Chirality : 0.183 1.551 720 Planarity : 0.001 0.008 670 Dihedral : 5.274 15.591 580 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Rotamer: Outliers : 4.00 % Allowed : 11.75 % Favored : 84.25 % 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: -3.74 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 50 PHE 0.016 0.002 PHE C 94 TYR 0.003 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.01973 ( 60) hydrogen bonds : angle 3.97523 ( 180) covalent geometry : bond 0.00306 ( 3980) covalent geometry : angle 0.78752 ( 5400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.566 Fit side-chains REVERT: H 57 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7553 (tp30) REVERT: H 83 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6824 (mm-30) REVERT: I 46 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7573 (mt-10) REVERT: J 46 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: J 83 GLU cc_start: 0.7514 (mp0) cc_final: 0.7148 (mp0) outliers start: 16 outliers final: 15 residues processed: 51 average time/residue: 0.1705 time to fit residues: 13.2343 Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 0.0170 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- 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 = 0.4790 r_free = 0.4790 target = 0.209537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.180348 restraints weight = 13848.383| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 2.94 r_work: 0.4414 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3980 Z= 0.199 Angle : 0.836 10.964 5400 Z= 0.454 Chirality : 0.183 1.550 720 Planarity : 0.002 0.009 670 Dihedral : 5.723 17.276 580 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.86 % Favored : 82.14 % Rotamer: Outliers : 4.25 % Allowed : 11.50 % Favored : 84.25 % 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: -3.83 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.013 0.002 PHE J 94 TYR 0.003 0.000 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02499 ( 60) hydrogen bonds : angle 4.24407 ( 180) covalent geometry : bond 0.00424 ( 3980) covalent geometry : angle 0.83620 ( 5400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.44 seconds wall clock time: 66 minutes 30.53 seconds (3990.53 seconds total)