Starting phenix.real_space_refine on Wed Feb 12 12:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h6b_0148/02_2025/6h6b_0148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h6b_0148/02_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_0148/02_2025/6h6b_0148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h6b_0148/02_2025/6h6b_0148.map" model { file = "/net/cci-nas-00/data/ceres_data/6h6b_0148/02_2025/6h6b_0148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h6b_0148/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.96, per 1000 atoms: 0.49 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: 2.00 Conformation dependent library (CDL) restraints added in 692.9 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: 2.48 Time building geometry restraints manager: 2.39 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: 0.920 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: 0.150 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- 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= 0.545 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 *********************** 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 : 0.561 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: 0.1986 time to fit residues: 22.9480 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 : 0.573 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4936 r_free = 0.4936 target = 0.223915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.193838 restraints weight = 13948.187| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 2.82 r_work: 0.4576 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3980 Z= 0.223 Angle : 0.812 11.123 5400 Z= 0.437 Chirality : 0.182 1.559 720 Planarity : 0.002 0.009 670 Dihedral : 5.828 16.878 580 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.25 % Allowed : 7.25 % Favored : 92.50 % 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: -4.24 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.18), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.015 0.003 PHE D 94 TYR 0.004 0.001 TYR B 39 *********************** 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 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6864 (mm-30) REVERT: D 65 ASN cc_start: 0.6455 (t0) cc_final: 0.6107 (t0) REVERT: G 65 ASN cc_start: 0.7531 (t0) cc_final: 0.7157 (t0) REVERT: I 65 ASN cc_start: 0.7845 (t0) cc_final: 0.7642 (t0) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.1803 time to fit residues: 15.7470 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4780 r_free = 0.4780 target = 0.209857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.180235 restraints weight = 14048.332| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 3.06 r_work: 0.4413 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3980 Z= 0.366 Angle : 0.917 11.254 5400 Z= 0.500 Chirality : 0.188 1.610 720 Planarity : 0.003 0.011 670 Dihedral : 6.629 21.004 580 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 1.50 % Allowed : 8.00 % Favored : 90.50 % 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: -3.96 (0.25), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS I 50 PHE 0.011 0.003 PHE A 94 TYR 0.002 0.000 TYR F 39 *********************** 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 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.596 Fit side-chains REVERT: A 94 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.6183 (m-10) REVERT: B 46 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: B 83 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6900 (mm-30) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.1724 time to fit residues: 15.1977 Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 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 = 0.4800 r_free = 0.4800 target = 0.212922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.184203 restraints weight = 13896.490| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.85 r_work: 0.4430 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3980 Z= 0.299 Angle : 0.861 11.047 5400 Z= 0.467 Chirality : 0.183 1.567 720 Planarity : 0.002 0.006 670 Dihedral : 6.169 19.078 580 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 5.00 % Allowed : 9.25 % Favored : 85.75 % 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 0.005 0.002 HIS G 50 PHE 0.010 0.002 PHE E 94 TYR 0.003 0.001 TYR F 39 *********************** 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 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.662 Fit side-chains REVERT: B 46 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: J 83 GLU cc_start: 0.7337 (mp0) cc_final: 0.6987 (mp0) outliers start: 20 outliers final: 16 residues processed: 53 average time/residue: 0.1845 time to fit residues: 14.6701 Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 46 GLU 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 I residue 75 THR 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: 5.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.4800 r_free = 0.4800 target = 0.210718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.180533 restraints weight = 13714.719| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.96 r_work: 0.4428 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4650 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= 0.286 Angle : 0.838 11.084 5400 Z= 0.454 Chirality : 0.184 1.577 720 Planarity : 0.002 0.005 670 Dihedral : 5.992 17.810 580 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % Rotamer: Outliers : 4.75 % Allowed : 10.25 % Favored : 85.00 % 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: -3.76 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 50 PHE 0.010 0.002 PHE D 94 TYR 0.002 0.000 TYR F 39 *********************** 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: 19 poor density : 44 time to evaluate : 0.631 Fit side-chains REVERT: B 46 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: H 57 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7569 (tp30) outliers start: 19 outliers final: 18 residues processed: 53 average time/residue: 0.1895 time to fit residues: 15.2300 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 46 GLU 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 I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL 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: 10.0000 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 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 = 0.4781 r_free = 0.4781 target = 0.209313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.179635 restraints weight = 13906.597| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.02 r_work: 0.4404 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4946 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= 0.319 Angle : 0.863 11.034 5400 Z= 0.469 Chirality : 0.184 1.578 720 Planarity : 0.002 0.007 670 Dihedral : 6.093 18.401 580 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.82 % Favored : 80.18 % Rotamer: Outliers : 5.00 % Allowed : 11.25 % Favored : 83.75 % 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: -3.82 (0.28), 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 0.006 0.002 HIS I 50 PHE 0.009 0.002 PHE D 94 TYR 0.003 0.000 TYR F 39 *********************** 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 64 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.638 Fit side-chains REVERT: B 46 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: D 83 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6760 (mm-30) REVERT: J 83 GLU cc_start: 0.7450 (mp0) cc_final: 0.7113 (mp0) outliers start: 20 outliers final: 19 residues processed: 54 average time/residue: 0.1822 time to fit residues: 14.7742 Evaluate side-chains 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 46 GLU 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 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR 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: 1.9990 chunk 33 optimal weight: 0.0000 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.209214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.179352 restraints weight = 13969.462| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 3.03 r_work: 0.4410 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5080 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= 0.292 Angle : 0.840 11.008 5400 Z= 0.456 Chirality : 0.184 1.564 720 Planarity : 0.002 0.008 670 Dihedral : 5.958 17.484 580 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 4.75 % Allowed : 11.75 % Favored : 83.50 % 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: -3.89 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.017 0.002 PHE C 94 TYR 0.003 0.000 TYR F 39 *********************** 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 : 0.578 Fit side-chains REVERT: B 46 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: D 83 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6852 (mm-30) REVERT: H 57 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7567 (tp30) REVERT: J 83 GLU cc_start: 0.7417 (mp0) cc_final: 0.7053 (mp0) outliers start: 19 outliers final: 18 residues processed: 55 average time/residue: 0.1809 time to fit residues: 15.0531 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 : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 46 GLU 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 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 75 THR Chi-restraints excluded: chain I residue 94 PHE 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4813 r_free = 0.4813 target = 0.211605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.182174 restraints weight = 13805.002| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.95 r_work: 0.4445 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5185 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= 0.237 Angle : 0.802 11.064 5400 Z= 0.432 Chirality : 0.184 1.556 720 Planarity : 0.001 0.006 670 Dihedral : 5.572 15.917 580 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % Rotamer: Outliers : 4.00 % Allowed : 12.75 % Favored : 83.25 % 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: -3.88 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 50 PHE 0.012 0.002 PHE C 94 TYR 0.003 0.000 TYR F 39 *********************** 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 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.497 Fit side-chains REVERT: A 66 VAL cc_start: 0.8323 (t) cc_final: 0.7886 (m) REVERT: B 46 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: H 57 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7520 (tp30) REVERT: J 83 GLU cc_start: 0.7447 (mp0) cc_final: 0.7079 (mp0) outliers start: 16 outliers final: 14 residues processed: 56 average time/residue: 0.1902 time to fit residues: 16.1706 Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 46 GLU 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 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 75 THR 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4817 r_free = 0.4817 target = 0.211587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.182022 restraints weight = 13868.354| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 2.98 r_work: 0.4446 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5262 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= 0.246 Angle : 0.804 11.055 5400 Z= 0.434 Chirality : 0.184 1.561 720 Planarity : 0.002 0.006 670 Dihedral : 5.533 16.088 580 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 4.25 % Allowed : 11.75 % Favored : 84.00 % 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: -3.84 (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 0.003 0.001 HIS I 50 PHE 0.013 0.002 PHE C 94 TYR 0.003 0.000 TYR F 39 *********************** 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 61 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.618 Fit side-chains REVERT: A 66 VAL cc_start: 0.8346 (t) cc_final: 0.7909 (m) REVERT: B 46 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: H 57 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7533 (tp30) REVERT: J 83 GLU cc_start: 0.7429 (mp0) cc_final: 0.7046 (mp0) outliers start: 17 outliers final: 15 residues processed: 53 average time/residue: 0.1903 time to fit residues: 15.3080 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 : 0.683 ------------------------------------------------------------------------------- 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 46 GLU 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 D residue 75 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 75 THR Chi-restraints excluded: chain I residue 94 PHE Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4876 r_free = 0.4876 target = 0.217567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.187986 restraints weight = 13624.043| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.97 r_work: 0.4509 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5327 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= 0.200 Angle : 0.759 11.318 5400 Z= 0.406 Chirality : 0.184 1.575 720 Planarity : 0.001 0.008 670 Dihedral : 4.935 13.916 580 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 2.00 % Allowed : 13.75 % 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: -3.69 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.015 0.002 PHE C 94 TYR 0.003 0.001 TYR B 39 ********************** 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 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.640 Fit side-chains REVERT: A 66 VAL cc_start: 0.8264 (t) cc_final: 0.7857 (m) REVERT: B 46 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 75 THR cc_start: 0.7654 (m) cc_final: 0.7441 (m) REVERT: H 57 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7590 (tp30) REVERT: J 83 GLU cc_start: 0.7410 (mp0) cc_final: 0.7038 (mp0) outliers start: 8 outliers final: 8 residues processed: 49 average time/residue: 0.2067 time to fit residues: 15.2334 Evaluate side-chains 52 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 54 THR 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: 7.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.4778 r_free = 0.4778 target = 0.207974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.178944 restraints weight = 13819.741| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.02 r_work: 0.4399 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3980 Z= 0.368 Angle : 0.876 10.989 5400 Z= 0.479 Chirality : 0.183 1.562 720 Planarity : 0.002 0.013 670 Dihedral : 5.919 19.220 580 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.86 % Favored : 82.14 % Rotamer: Outliers : 2.75 % Allowed : 13.25 % Favored : 84.00 % 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: -3.86 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 50 PHE 0.008 0.002 PHE D 94 TYR 0.004 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.96 seconds wall clock time: 65 minutes 16.80 seconds (3916.80 seconds total)