Starting phenix.real_space_refine on Wed Sep 17 09:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h6b_0148/09_2025/6h6b_0148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h6b_0148/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6h6b_0148/09_2025/6h6b_0148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h6b_0148/09_2025/6h6b_0148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6h6b_0148/09_2025/6h6b_0148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h6b_0148/09_2025/6h6b_0148.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.68, per 1000 atoms: 0.21 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: 0.71 Conformation dependent library (CDL) restraints added in 339.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 1.85 Time building geometry restraints manager: 1.02 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 1.550 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.80 (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 TYR 0.002 0.001 TYR I 39 PHE 0.007 0.003 PHE D 94 HIS 0.008 0.005 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 3980) covalent geometry : angle 1.10061 ( 5400) hydrogen bonds : bond 0.24005 ( 60) hydrogen bonds : angle 9.01586 ( 180) *********************** 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 : 0.209 Fit side-chains revert: symmetry clash REVERT: C 54 THR cc_start: 0.6415 (m) cc_final: 0.6196 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0759 time to fit residues: 9.1063 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 : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4888 r_free = 0.4888 target = 0.219507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.189051 restraints weight = 13917.596| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.90 r_work: 0.4524 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3980 Z= 0.140 Angle : 0.836 11.104 5400 Z= 0.452 Chirality : 0.183 1.567 720 Planarity : 0.002 0.010 670 Dihedral : 6.071 17.972 580 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.25 % Allowed : 8.25 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.23), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.18), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.015 0.003 PHE D 94 HIS 0.003 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3980) covalent geometry : angle 0.83639 ( 5400) hydrogen bonds : bond 0.03342 ( 60) hydrogen bonds : angle 4.45943 ( 180) *********************** 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 61 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 83 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6901 (mm-30) REVERT: D 83 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6756 (mm-30) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.0814 time to fit residues: 7.3646 Evaluate side-chains 50 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.221684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.191427 restraints weight = 13462.588| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 2.96 r_work: 0.4523 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3278 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= 0.119 Angle : 0.797 11.289 5400 Z= 0.428 Chirality : 0.185 1.566 720 Planarity : 0.002 0.007 670 Dihedral : 5.464 15.555 580 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 1.00 % Allowed : 9.75 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.25), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR E 39 PHE 0.017 0.002 PHE E 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3980) covalent geometry : angle 0.79713 ( 5400) hydrogen bonds : bond 0.02898 ( 60) hydrogen bonds : angle 3.84499 ( 180) *********************** 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 54 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.220 Fit side-chains REVERT: B 83 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7049 (mm-30) REVERT: H 83 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6621 (mm-30) REVERT: I 46 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7137 (mt-10) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0815 time to fit residues: 6.2903 Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4810 r_free = 0.4810 target = 0.213992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.183989 restraints weight = 14075.445| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 3.11 r_work: 0.4443 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3980 Z= 0.178 Angle : 0.841 11.131 5400 Z= 0.455 Chirality : 0.184 1.571 720 Planarity : 0.002 0.007 670 Dihedral : 5.828 18.470 580 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 4.75 % Allowed : 8.00 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.26), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 39 PHE 0.008 0.002 PHE A 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3980) covalent geometry : angle 0.84062 ( 5400) hydrogen bonds : bond 0.02574 ( 60) hydrogen bonds : angle 3.80728 ( 180) *********************** 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 73 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.217 Fit side-chains REVERT: D 83 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6779 (mm-30) REVERT: G 46 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6867 (tt0) REVERT: H 57 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7668 (tp30) REVERT: I 46 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7455 (mt-10) REVERT: J 46 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: J 83 GLU cc_start: 0.7309 (mp0) cc_final: 0.6989 (mp0) outliers start: 19 outliers final: 17 residues processed: 60 average time/residue: 0.0755 time to fit residues: 7.0009 Evaluate side-chains 69 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 C residue 77 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 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 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 18 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4777 r_free = 0.4777 target = 0.209002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.179849 restraints weight = 14011.628| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.97 r_work: 0.4413 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3980 Z= 0.231 Angle : 0.888 11.076 5400 Z= 0.484 Chirality : 0.184 1.596 720 Planarity : 0.002 0.007 670 Dihedral : 6.340 20.731 580 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer: Outliers : 5.75 % Allowed : 9.75 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR F 39 PHE 0.010 0.002 PHE E 94 HIS 0.007 0.003 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 3980) covalent geometry : angle 0.88769 ( 5400) hydrogen bonds : bond 0.03096 ( 60) hydrogen bonds : angle 4.36031 ( 180) *********************** 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 74 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.208 Fit side-chains REVERT: A 57 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7489 (tp30) REVERT: D 83 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6681 (mm-30) REVERT: I 46 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7688 (mt-10) REVERT: J 46 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7263 (mt-10) outliers start: 23 outliers final: 20 residues processed: 64 average time/residue: 0.0774 time to fit residues: 7.6236 Evaluate side-chains 66 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL 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 C residue 77 VAL 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 F residue 75 THR 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 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 23 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4859 r_free = 0.4859 target = 0.216642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.186689 restraints weight = 13738.065| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 3.01 r_work: 0.4484 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4752 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= 0.109 Angle : 0.780 11.122 5400 Z= 0.419 Chirality : 0.181 1.552 720 Planarity : 0.001 0.005 670 Dihedral : 5.366 15.958 580 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 3.25 % Allowed : 13.75 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.60 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.012 0.001 PHE D 94 HIS 0.002 0.000 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3980) covalent geometry : angle 0.77991 ( 5400) hydrogen bonds : bond 0.01875 ( 60) hydrogen bonds : angle 3.84789 ( 180) *********************** 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: 13 poor density : 50 time to evaluate : 0.150 Fit side-chains REVERT: I 46 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7591 (mt-10) REVERT: J 83 GLU cc_start: 0.7336 (mp0) cc_final: 0.6942 (mp0) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.0727 time to fit residues: 6.0524 Evaluate side-chains 59 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 77 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 Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4795 r_free = 0.4795 target = 0.210949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.181301 restraints weight = 13970.534| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.98 r_work: 0.4421 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4937 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= 0.206 Angle : 0.843 10.998 5400 Z= 0.458 Chirality : 0.184 1.567 720 Planarity : 0.002 0.006 670 Dihedral : 5.841 17.888 580 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % Rotamer: Outliers : 3.75 % Allowed : 14.25 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR F 39 PHE 0.009 0.002 PHE A 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3980) covalent geometry : angle 0.84310 ( 5400) hydrogen bonds : bond 0.02738 ( 60) hydrogen bonds : angle 4.17299 ( 180) *********************** 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 60 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.227 Fit side-chains REVERT: I 46 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7613 (mt-10) REVERT: J 46 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: J 83 GLU cc_start: 0.7478 (mp0) cc_final: 0.7086 (mp0) outliers start: 15 outliers final: 13 residues processed: 57 average time/residue: 0.0759 time to fit residues: 6.7205 Evaluate side-chains 57 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 77 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 54 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 2 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4784 r_free = 0.4784 target = 0.209608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.180927 restraints weight = 13922.171| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 2.93 r_work: 0.4421 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3980 Z= 0.213 Angle : 0.858 10.951 5400 Z= 0.466 Chirality : 0.184 1.560 720 Planarity : 0.002 0.006 670 Dihedral : 6.051 18.426 580 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.82 % Favored : 80.18 % Rotamer: Outliers : 5.50 % Allowed : 13.00 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.90 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR F 39 PHE 0.008 0.002 PHE E 94 HIS 0.006 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3980) covalent geometry : angle 0.85761 ( 5400) hydrogen bonds : bond 0.02715 ( 60) hydrogen bonds : angle 4.23003 ( 180) *********************** 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 65 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.272 Fit side-chains REVERT: D 83 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6780 (mm-30) REVERT: I 46 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7619 (mt-10) REVERT: J 46 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: J 83 GLU cc_start: 0.7515 (mp0) cc_final: 0.7126 (mp0) outliers start: 22 outliers final: 19 residues processed: 58 average time/residue: 0.0772 time to fit residues: 6.9998 Evaluate side-chains 63 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4870 r_free = 0.4870 target = 0.217290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.187771 restraints weight = 13829.382| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 3.03 r_work: 0.4498 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3980 Z= 0.106 Angle : 0.766 11.218 5400 Z= 0.410 Chirality : 0.183 1.579 720 Planarity : 0.001 0.006 670 Dihedral : 5.134 15.202 580 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.00 % Allowed : 15.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.27), 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 TYR 0.003 0.001 TYR F 39 PHE 0.013 0.001 PHE D 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3980) covalent geometry : angle 0.76585 ( 5400) hydrogen bonds : bond 0.01829 ( 60) hydrogen bonds : angle 3.84345 ( 180) *********************** 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 62 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.223 Fit side-chains REVERT: H 72 THR cc_start: 0.8607 (p) cc_final: 0.8161 (m) REVERT: I 46 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7542 (mt-10) REVERT: J 83 GLU cc_start: 0.7425 (mp0) cc_final: 0.7059 (mp0) outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.0759 time to fit residues: 6.5711 Evaluate side-chains 57 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D 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 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 26 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4793 r_free = 0.4793 target = 0.210126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.180968 restraints weight = 13868.353| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.97 r_work: 0.4434 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3980 Z= 0.219 Angle : 0.853 10.880 5400 Z= 0.465 Chirality : 0.183 1.552 720 Planarity : 0.002 0.008 670 Dihedral : 5.852 17.538 580 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer: Outliers : 3.25 % Allowed : 14.50 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 39 PHE 0.009 0.002 PHE A 94 HIS 0.005 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 3980) covalent geometry : angle 0.85265 ( 5400) hydrogen bonds : bond 0.02749 ( 60) hydrogen bonds : angle 4.30525 ( 180) ********************** 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 56 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.212 Fit side-chains REVERT: I 46 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7620 (mt-10) REVERT: J 83 GLU cc_start: 0.7544 (mp0) cc_final: 0.7136 (mp0) outliers start: 13 outliers final: 13 residues processed: 52 average time/residue: 0.0750 time to fit residues: 6.0178 Evaluate side-chains 56 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B 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 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 3 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 10.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 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 = 0.4828 r_free = 0.4828 target = 0.213040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.184231 restraints weight = 13789.557| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.95 r_work: 0.4454 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3980 Z= 0.147 Angle : 0.802 10.994 5400 Z= 0.433 Chirality : 0.183 1.546 720 Planarity : 0.002 0.012 670 Dihedral : 5.536 16.190 580 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 3.25 % Allowed : 13.75 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR F 39 PHE 0.009 0.002 PHE D 94 HIS 0.004 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3980) covalent geometry : angle 0.80206 ( 5400) hydrogen bonds : bond 0.02221 ( 60) hydrogen bonds : angle 4.10308 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.00 seconds wall clock time: 36 minutes 16.54 seconds (2176.54 seconds total)