Starting phenix.real_space_refine on Tue Sep 24 10:52:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_0148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_0148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_0148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_0148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/09_2024/6h6b_0148.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 2480 2.51 5 N 680 2.21 5 O 800 1.98 5 H 4100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 806 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 4.17, per 1000 atoms: 0.52 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: 2.14 Conformation dependent library (CDL) restraints added in 747.7 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: 0.81 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: 2.45 Time building geometry restraints manager: 2.56 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain '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: 2.010 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.900 Find NCS groups from input model: 0.210 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.533 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: 0.2004 time to fit residues: 23.7676 Evaluate side-chains 54 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: D 65 ASN cc_start: 0.6570 (t0) cc_final: 0.6214 (t0) REVERT: G 65 ASN cc_start: 0.7375 (t0) cc_final: 0.6992 (t0) REVERT: I 65 ASN cc_start: 0.7800 (t0) cc_final: 0.7504 (t0) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.1845 time to fit residues: 15.9864 Evaluate side-chains 49 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3980 Z= 0.313 Angle : 0.877 11.373 5400 Z= 0.475 Chirality : 0.187 1.591 720 Planarity : 0.002 0.015 670 Dihedral : 6.311 18.620 580 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.89 % Favored : 84.11 % Rotamer: Outliers : 1.25 % Allowed : 7.50 % Favored : 91.25 % 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: -3.95 (0.25), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS I 50 PHE 0.009 0.002 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 62 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.571 Fit side-chains REVERT: I 46 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6634 (mt-10) outliers start: 5 outliers final: 1 residues processed: 58 average time/residue: 0.1760 time to fit residues: 15.2135 Evaluate side-chains 46 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4131 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= 0.238 Angle : 0.817 11.065 5400 Z= 0.441 Chirality : 0.183 1.576 720 Planarity : 0.002 0.009 670 Dihedral : 5.735 18.145 580 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 4.25 % Allowed : 8.25 % Favored : 87.50 % 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: -3.74 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 50 PHE 0.022 0.002 PHE A 94 TYR 0.002 0.000 TYR C 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 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.642 Fit side-chains REVERT: I 46 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6210 (tt0) outliers start: 17 outliers final: 16 residues processed: 54 average time/residue: 0.1893 time to fit residues: 15.9374 Evaluate side-chains 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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 J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4630 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= 0.332 Angle : 0.870 11.112 5400 Z= 0.473 Chirality : 0.185 1.597 720 Planarity : 0.002 0.006 670 Dihedral : 6.140 22.142 580 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % 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: -3.71 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS I 50 PHE 0.009 0.002 PHE A 94 TYR 0.002 0.000 TYR C 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 64 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.653 Fit side-chains REVERT: I 46 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6788 (mt-10) REVERT: J 83 GLU cc_start: 0.7342 (mp0) cc_final: 0.7059 (mp0) outliers start: 19 outliers final: 19 residues processed: 57 average time/residue: 0.1781 time to fit residues: 15.3718 Evaluate side-chains 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain 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 Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3980 Z= 0.393 Angle : 0.913 10.921 5400 Z= 0.500 Chirality : 0.185 1.611 720 Planarity : 0.002 0.007 670 Dihedral : 6.480 25.424 580 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.18 % Favored : 79.82 % Rotamer: Outliers : 5.25 % Allowed : 11.75 % 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 (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: -3.95 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS I 50 PHE 0.009 0.002 PHE C 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 70 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.634 Fit side-chains REVERT: I 46 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6711 (mt-10) outliers start: 21 outliers final: 21 residues processed: 62 average time/residue: 0.1742 time to fit residues: 16.2191 Evaluate side-chains 63 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 42 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5125 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= 0.222 Angle : 0.789 11.007 5400 Z= 0.425 Chirality : 0.180 1.542 720 Planarity : 0.001 0.006 670 Dihedral : 5.568 17.258 580 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 3.00 % Allowed : 14.25 % Favored : 82.75 % 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: -3.78 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.013 0.002 PHE D 94 TYR 0.004 0.001 TYR C 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 60 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.589 Fit side-chains REVERT: A 66 VAL cc_start: 0.8347 (t) cc_final: 0.8031 (m) REVERT: H 72 THR cc_start: 0.8329 (p) cc_final: 0.7916 (m) REVERT: I 46 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6648 (mt-10) outliers start: 12 outliers final: 12 residues processed: 55 average time/residue: 0.1775 time to fit residues: 14.6341 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5208 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= 0.217 Angle : 0.778 11.080 5400 Z= 0.418 Chirality : 0.181 1.545 720 Planarity : 0.001 0.006 670 Dihedral : 5.224 15.952 580 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % 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 (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 0.004 0.001 HIS I 50 PHE 0.013 0.001 PHE D 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 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.564 Fit side-chains REVERT: A 66 VAL cc_start: 0.8346 (t) cc_final: 0.8036 (m) REVERT: I 46 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6698 (mt-10) REVERT: J 83 GLU cc_start: 0.7173 (mp0) cc_final: 0.6947 (mp0) outliers start: 13 outliers final: 13 residues processed: 54 average time/residue: 0.1744 time to fit residues: 14.1357 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5286 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= 0.213 Angle : 0.769 11.061 5400 Z= 0.413 Chirality : 0.180 1.527 720 Planarity : 0.001 0.007 670 Dihedral : 5.110 17.455 580 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % Rotamer: Outliers : 3.25 % Allowed : 14.25 % Favored : 82.50 % 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: -3.62 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.012 0.001 PHE D 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 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.607 Fit side-chains REVERT: A 66 VAL cc_start: 0.8346 (t) cc_final: 0.8033 (m) REVERT: I 46 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6683 (mt-10) outliers start: 13 outliers final: 13 residues processed: 49 average time/residue: 0.1675 time to fit residues: 12.6127 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5360 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= 0.229 Angle : 0.781 11.014 5400 Z= 0.420 Chirality : 0.180 1.525 720 Planarity : 0.001 0.007 670 Dihedral : 5.172 16.522 580 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % 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 (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: -3.64 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 50 PHE 0.011 0.001 PHE D 94 TYR 0.003 0.000 TYR F 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 55 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.631 Fit side-chains REVERT: A 66 VAL cc_start: 0.8357 (t) cc_final: 0.8038 (m) REVERT: I 46 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6700 (mt-10) outliers start: 13 outliers final: 13 residues processed: 50 average time/residue: 0.1682 time to fit residues: 12.9004 Evaluate side-chains 53 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4819 r_free = 0.4819 target = 0.211671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.182510 restraints weight = 13789.678| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 2.94 r_work: 0.4451 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5438 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= 0.266 Angle : 0.808 10.968 5400 Z= 0.437 Chirality : 0.181 1.531 720 Planarity : 0.002 0.009 670 Dihedral : 5.445 17.720 580 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.32 % Favored : 82.68 % Rotamer: Outliers : 3.75 % Allowed : 14.00 % 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 (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: -3.72 (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 HIS 0.004 0.001 HIS I 50 PHE 0.010 0.002 PHE D 94 TYR 0.003 0.000 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.42 seconds wall clock time: 41 minutes 43.10 seconds (2503.10 seconds total)