Starting phenix.real_space_refine on Mon Mar 11 10:32:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/03_2024/6h6b_0148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/03_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_0148/03_2024/6h6b_0148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/03_2024/6h6b_0148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/03_2024/6h6b_0148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6b_0148/03_2024/6h6b_0148.pdb" } 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 Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.98, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 6.52 Conformation dependent library (CDL) restraints added in 910.3 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: 0.74 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: 2.52 Time building geometry restraints manager: 6.73 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: 83.12 - 92.71: 30 92.71 - 102.31: 0 102.31 - 111.90: 9868 111.90 - 121.50: 3005 121.50 - 131.09: 1757 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 1.850 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 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 4.760 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.580 Find NCS groups from input model: 0.370 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- 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 : 0.607 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: 0.1715 time to fit residues: 19.8906 Evaluate side-chains 54 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3980 Z= 0.221 Angle : 0.808 11.125 5400 Z= 0.435 Chirality : 0.181 1.555 720 Planarity : 0.002 0.009 670 Dihedral : 5.814 17.655 580 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 0.25 % Allowed : 7.50 % Favored : 92.25 % 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: -4.25 (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 0.002 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 58 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6388 (mm-30) REVERT: D 65 ASN cc_start: 0.6759 (t0) cc_final: 0.6478 (t0) REVERT: G 65 ASN cc_start: 0.7493 (t0) cc_final: 0.7123 (t0) REVERT: I 65 ASN cc_start: 0.7805 (t0) cc_final: 0.7490 (t0) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1766 time to fit residues: 14.8746 Evaluate side-chains 49 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3980 Z= 0.425 Angle : 0.946 11.165 5400 Z= 0.517 Chirality : 0.189 1.634 720 Planarity : 0.003 0.009 670 Dihedral : 6.903 23.423 580 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 1.75 % Allowed : 10.00 % Favored : 88.25 % 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: -4.05 (0.25), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS I 50 PHE 0.014 0.003 PHE A 94 TYR 0.002 0.000 TYR A 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 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.660 Fit side-chains REVERT: B 83 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6649 (mm-30) REVERT: I 46 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6803 (mt-10) REVERT: J 46 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6257 (mm-30) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.1886 time to fit residues: 18.4311 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.4227 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= 0.245 Angle : 0.819 11.107 5400 Z= 0.443 Chirality : 0.181 1.565 720 Planarity : 0.002 0.007 670 Dihedral : 5.962 18.449 580 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 4.25 % Allowed : 9.75 % Favored : 86.00 % 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: -3.81 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.011 0.002 PHE D 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 67 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.619 Fit side-chains REVERT: I 46 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6660 (mt-10) REVERT: J 46 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6383 (mm-30) outliers start: 17 outliers final: 15 residues processed: 56 average time/residue: 0.1791 time to fit residues: 14.9719 Evaluate side-chains 66 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 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 77 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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: 0.7557 moved from start: 0.4602 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= 0.324 Angle : 0.864 11.132 5400 Z= 0.470 Chirality : 0.184 1.593 720 Planarity : 0.002 0.007 670 Dihedral : 6.165 18.808 580 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer: Outliers : 5.75 % Allowed : 10.25 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS I 50 PHE 0.009 0.002 PHE A 94 TYR 0.003 0.000 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 48 time to evaluate : 0.624 Fit side-chains REVERT: I 46 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6873 (mt-10) REVERT: J 46 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6433 (mm-30) outliers start: 23 outliers final: 18 residues processed: 62 average time/residue: 0.1680 time to fit residues: 15.7848 Evaluate side-chains 65 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3980 Z= 0.262 Angle : 0.824 11.099 5400 Z= 0.446 Chirality : 0.182 1.565 720 Planarity : 0.002 0.007 670 Dihedral : 5.800 16.920 580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Rotamer: Outliers : 4.50 % Allowed : 11.25 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.011 0.002 PHE D 94 TYR 0.003 0.000 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.638 Fit side-chains REVERT: I 46 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6745 (mt-10) REVERT: J 46 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6355 (mm-30) outliers start: 18 outliers final: 17 residues processed: 54 average time/residue: 0.1774 time to fit residues: 14.4374 Evaluate side-chains 61 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 74 VAL 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 46 GLU 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 27 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.5032 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= 0.231 Angle : 0.793 11.121 5400 Z= 0.428 Chirality : 0.182 1.552 720 Planarity : 0.001 0.005 670 Dihedral : 5.435 16.304 580 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % Rotamer: Outliers : 2.75 % Allowed : 13.00 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 50 PHE 0.012 0.001 PHE D 94 TYR 0.003 0.000 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.642 Fit side-chains REVERT: I 46 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6741 (mt-10) REVERT: J 46 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6387 (mm-30) outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.1735 time to fit residues: 13.3944 Evaluate side-chains 57 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 55 VAL 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 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 23 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.5214 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= 0.335 Angle : 0.863 10.993 5400 Z= 0.471 Chirality : 0.183 1.566 720 Planarity : 0.002 0.006 670 Dihedral : 5.961 18.454 580 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.18 % Favored : 79.82 % Rotamer: Outliers : 4.75 % Allowed : 11.50 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.27), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 50 PHE 0.009 0.002 PHE A 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: 19 poor density : 42 time to evaluate : 0.569 Fit side-chains REVERT: I 46 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6886 (mt-10) REVERT: J 46 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6386 (mm-30) outliers start: 19 outliers final: 18 residues processed: 54 average time/residue: 0.1691 time to fit residues: 13.8967 Evaluate side-chains 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 55 VAL 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 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 94 PHE Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.7486 moved from start: 0.5251 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= 0.211 Angle : 0.772 11.117 5400 Z= 0.415 Chirality : 0.182 1.558 720 Planarity : 0.001 0.006 670 Dihedral : 5.154 15.327 580 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 2.50 % Allowed : 13.50 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 PHE 0.013 0.001 PHE D 94 TYR 0.003 0.001 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 59 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.645 Fit side-chains REVERT: A 66 VAL cc_start: 0.8393 (t) cc_final: 0.8062 (m) REVERT: H 72 THR cc_start: 0.8413 (p) cc_final: 0.8048 (m) REVERT: I 46 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6727 (mt-10) REVERT: J 83 GLU cc_start: 0.7130 (mp0) cc_final: 0.6837 (mp0) outliers start: 10 outliers final: 10 residues processed: 53 average time/residue: 0.1791 time to fit residues: 14.3075 Evaluate side-chains 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 74 VAL 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 J residue 54 THR 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: 7.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.7508 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 0.031 3980 Z= 0.231 Angle : 0.786 11.036 5400 Z= 0.424 Chirality : 0.181 1.533 720 Planarity : 0.001 0.006 670 Dihedral : 5.217 15.856 580 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Rotamer: Outliers : 3.00 % Allowed : 13.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.28), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 56 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.636 Fit side-chains REVERT: A 83 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6366 (mm-30) REVERT: I 46 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6775 (mt-10) REVERT: J 83 GLU cc_start: 0.7139 (mp0) cc_final: 0.6865 (mp0) outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.1772 time to fit residues: 13.4202 Evaluate side-chains 54 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 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 75 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.4802 r_free = 0.4802 target = 0.209410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.180380 restraints weight = 13843.754| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.92 r_work: 0.4436 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 0.030 3980 Z= 0.271 Angle : 0.816 11.020 5400 Z= 0.442 Chirality : 0.182 1.542 720 Planarity : 0.002 0.006 670 Dihedral : 5.515 16.661 580 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % Rotamer: Outliers : 3.25 % Allowed : 12.75 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (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 HIS 0.004 0.002 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: 2360.15 seconds wall clock time: 42 minutes 20.90 seconds (2540.90 seconds total)