Starting phenix.real_space_refine on Thu Jul 2 09:38:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/07_2026/8wv4_37864.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 20 5.16 5 C 5290 2.51 5 N 1305 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1632 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.39, per 1000 atoms: 0.17 Number of scatterers: 8170 At special positions: 0 Unit cell: (113.42, 115.56, 52.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 20 16.00 O 1545 8.00 N 1305 7.00 C 5290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 436.7 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 6.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE A 106 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 39 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 34 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS A 38 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 158 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 40 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE A 156 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN A 158 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N LYS A 7 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 85 removed outlier: 3.607A pdb=" N SER A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 52 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP A 67 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER A 50 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 55 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 133 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 20 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS A 191 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE B 106 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 39 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 34 " --> pdb=" O TRP B 162 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS B 38 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 158 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR B 40 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE B 156 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 158 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N LYS B 7 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER B 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 52 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 67 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER B 50 " --> pdb=" O TRP B 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 55 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 133 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 20 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 191 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE C 106 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 39 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 34 " --> pdb=" O TRP C 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS C 38 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN C 158 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR C 40 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE C 156 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN C 158 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS C 7 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 3.607A pdb=" N SER C 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 52 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP C 67 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER C 50 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 55 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 133 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 20 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS C 191 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE D 106 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 39 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 34 " --> pdb=" O TRP D 162 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS D 38 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN D 158 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 40 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE D 156 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN D 158 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS D 7 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER D 80 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 52 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP D 67 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER D 50 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 55 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 133 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 20 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS D 191 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.892A pdb=" N ILE E 106 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 39 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 34 " --> pdb=" O TRP E 162 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS E 38 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN E 158 " --> pdb=" O HIS E 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR E 40 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE E 156 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN E 158 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N LYS E 7 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.606A pdb=" N SER E 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 52 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP E 67 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER E 50 " --> pdb=" O TRP E 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA E 55 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 133 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 20 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS E 191 " --> pdb=" O LYS E 23 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2539 1.34 - 1.46: 2007 1.46 - 1.58: 3814 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 8390 Sorted by residual: bond pdb=" CB ASP D 60 " pdb=" CG ASP D 60 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASP A 60 " pdb=" CG ASP A 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP C 60 " pdb=" CG ASP C 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB ASP B 60 " pdb=" CG ASP B 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ASP E 60 " pdb=" CG ASP E 60 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 8385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 11043 1.20 - 2.39: 290 2.39 - 3.59: 62 3.59 - 4.78: 5 4.78 - 5.98: 5 Bond angle restraints: 11405 Sorted by residual: angle pdb=" N GLY C 72 " pdb=" CA GLY C 72 " pdb=" C GLY C 72 " ideal model delta sigma weight residual 110.20 113.10 -2.90 1.32e+00 5.74e-01 4.84e+00 angle pdb=" N GLY D 72 " pdb=" CA GLY D 72 " pdb=" C GLY D 72 " ideal model delta sigma weight residual 110.20 113.10 -2.90 1.32e+00 5.74e-01 4.83e+00 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 110.20 113.09 -2.89 1.32e+00 5.74e-01 4.81e+00 angle pdb=" N GLY E 72 " pdb=" CA GLY E 72 " pdb=" C GLY E 72 " ideal model delta sigma weight residual 110.20 113.09 -2.89 1.32e+00 5.74e-01 4.79e+00 angle pdb=" N GLY A 72 " pdb=" CA GLY A 72 " pdb=" C GLY A 72 " ideal model delta sigma weight residual 110.20 113.08 -2.88 1.32e+00 5.74e-01 4.77e+00 ... (remaining 11400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4525 17.50 - 35.00: 285 35.00 - 52.49: 35 52.49 - 69.99: 20 69.99 - 87.49: 30 Dihedral angle restraints: 4895 sinusoidal: 1940 harmonic: 2955 Sorted by residual: dihedral pdb=" CA PHE A 146 " pdb=" C PHE A 146 " pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE C 146 " pdb=" C PHE C 146 " pdb=" N GLU C 147 " pdb=" CA GLU C 147 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE D 146 " pdb=" C PHE D 146 " pdb=" N GLU D 147 " pdb=" CA GLU D 147 " ideal model delta harmonic sigma weight residual -180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 657 0.025 - 0.049: 312 0.049 - 0.074: 113 0.074 - 0.098: 68 0.098 - 0.123: 85 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CA ILE D 63 " pdb=" N ILE D 63 " pdb=" C ILE D 63 " pdb=" CB ILE D 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 63 " pdb=" N ILE A 63 " pdb=" C ILE A 63 " pdb=" CB ILE A 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1232 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 167 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO E 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO B 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A 168 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.016 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 146 2.53 - 3.12: 5808 3.12 - 3.72: 12054 3.72 - 4.31: 17672 4.31 - 4.90: 30425 Nonbonded interactions: 66105 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" OD1 ASN A 61 " model vdw 1.938 3.040 nonbonded pdb=" OD1 ASP C 60 " pdb=" OD1 ASN C 61 " model vdw 1.939 3.040 nonbonded pdb=" OD1 ASP E 60 " pdb=" OD1 ASN E 61 " model vdw 1.939 3.040 nonbonded pdb=" OD1 ASP B 60 " pdb=" OD1 ASN B 61 " model vdw 1.940 3.040 nonbonded pdb=" OD1 ASP D 60 " pdb=" OD1 ASN D 61 " model vdw 1.940 3.040 ... (remaining 66100 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.002 0.037 8395 Z= 0.112 Angle : 0.491 5.980 11415 Z= 0.287 Chirality : 0.044 0.123 1235 Planarity : 0.003 0.029 1450 Dihedral : 14.128 87.489 2990 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.33 % Allowed : 3.33 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.23), residues: 1020 helix: 1.99 (0.64), residues: 55 sheet: -1.44 (0.27), residues: 320 loop : -2.37 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 118 TYR 0.009 0.001 TYR A 54 PHE 0.009 0.001 PHE B 109 TRP 0.003 0.000 TRP D 110 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 8390) covalent geometry : angle 0.49079 / 0.29 (11405) SS BOND : bond 0.00039 / 0.02 ( 5) SS BOND : angle 0.02738 / 0.01 ( 10) hydrogen bonds : bond 0.28617 / 19.15 ( 290) hydrogen bonds : angle 8.32903 / 5.69 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.330 Fit side-chains REVERT: A 101 GLU cc_start: 0.8276 (tt0) cc_final: 0.7926 (tt0) REVERT: A 172 ASN cc_start: 0.8477 (t0) cc_final: 0.8259 (t0) REVERT: A 175 TYR cc_start: 0.8828 (t80) cc_final: 0.8555 (t80) REVERT: B 4 MET cc_start: 0.7729 (mtp) cc_final: 0.7506 (mtp) REVERT: B 62 GLU cc_start: 0.8034 (tp30) cc_final: 0.7804 (tp30) REVERT: B 137 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8086 (mm-40) REVERT: C 62 GLU cc_start: 0.8094 (tp30) cc_final: 0.7863 (tp30) REVERT: C 137 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8004 (mm-40) REVERT: C 175 TYR cc_start: 0.8830 (t80) cc_final: 0.8533 (t80) REVERT: D 62 GLU cc_start: 0.8029 (tp30) cc_final: 0.7267 (tp30) REVERT: D 125 TYR cc_start: 0.8633 (t80) cc_final: 0.7829 (t80) REVERT: D 137 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8190 (mm-40) REVERT: E 62 GLU cc_start: 0.8079 (tp30) cc_final: 0.7846 (tp30) REVERT: E 137 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8067 (mm-40) REVERT: E 172 ASN cc_start: 0.8602 (t0) cc_final: 0.8372 (t0) outliers start: 30 outliers final: 8 residues processed: 245 average time/residue: 0.0837 time to fit residues: 28.3442 Evaluate side-chains 163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 53 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN B 59 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 195 GLN C 59 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 195 GLN D 59 GLN E 59 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.081964 restraints weight = 12492.968| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.79 r_work: 0.2684 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8395 Z= 0.189 Angle : 0.548 4.038 11415 Z= 0.307 Chirality : 0.050 0.173 1235 Planarity : 0.004 0.033 1450 Dihedral : 4.518 33.137 1108 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 10.56 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.25), residues: 1020 helix: 2.71 (0.68), residues: 55 sheet: -1.04 (0.25), residues: 390 loop : -1.89 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 6 TYR 0.017 0.002 TYR B 54 PHE 0.011 0.002 PHE E 109 TRP 0.007 0.001 TRP A 205 HIS 0.007 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 8390) covalent geometry : angle 0.54854 / 0.31 (11405) SS BOND : bond 0.00105 / 0.05 ( 5) SS BOND : angle 0.49460 / 0.29 ( 10) hydrogen bonds : bond 0.04859 / 3.15 ( 290) hydrogen bonds : angle 5.66275 / 3.87 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.309 Fit side-chains REVERT: A 101 GLU cc_start: 0.8694 (tt0) cc_final: 0.8456 (tt0) REVERT: A 172 ASN cc_start: 0.8584 (t0) cc_final: 0.8364 (t0) REVERT: A 175 TYR cc_start: 0.8952 (t80) cc_final: 0.8639 (t80) REVERT: B 59 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7876 (tp-100) REVERT: B 101 GLU cc_start: 0.8580 (tt0) cc_final: 0.8374 (tt0) REVERT: B 137 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8101 (mm-40) REVERT: C 137 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8050 (mm-40) REVERT: D 16 ASP cc_start: 0.8510 (p0) cc_final: 0.8287 (p0) REVERT: D 62 GLU cc_start: 0.8654 (tp30) cc_final: 0.7927 (tp30) REVERT: D 125 TYR cc_start: 0.8849 (t80) cc_final: 0.7996 (t80) REVERT: E 137 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8320 (mm-40) REVERT: E 163 ASP cc_start: 0.8270 (p0) cc_final: 0.8046 (p0) REVERT: E 172 ASN cc_start: 0.8687 (t0) cc_final: 0.8472 (t0) outliers start: 6 outliers final: 2 residues processed: 173 average time/residue: 0.0927 time to fit residues: 22.0664 Evaluate side-chains 144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain E residue 130 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN C 139 GLN C 195 GLN D 195 GLN E 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.083564 restraints weight = 12472.310| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.82 r_work: 0.2661 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8395 Z= 0.116 Angle : 0.496 4.274 11415 Z= 0.275 Chirality : 0.048 0.168 1235 Planarity : 0.003 0.028 1450 Dihedral : 3.908 15.169 1100 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.78 % Allowed : 11.00 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 1020 helix: 3.01 (0.68), residues: 55 sheet: -0.71 (0.32), residues: 280 loop : -1.37 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 6 TYR 0.015 0.001 TYR B 54 PHE 0.014 0.001 PHE A 180 TRP 0.005 0.001 TRP C 162 HIS 0.002 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8390) covalent geometry : angle 0.49540 / 0.27 (11405) SS BOND : bond 0.00302 / 0.18 ( 5) SS BOND : angle 0.68243 / 0.40 ( 10) hydrogen bonds : bond 0.04410 / 2.87 ( 290) hydrogen bonds : angle 5.30877 / 3.64 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.306 Fit side-chains REVERT: A 101 GLU cc_start: 0.8649 (tt0) cc_final: 0.8256 (tt0) REVERT: A 147 GLU cc_start: 0.7368 (tt0) cc_final: 0.6948 (mt-10) REVERT: A 172 ASN cc_start: 0.8590 (t0) cc_final: 0.8384 (t0) REVERT: A 175 TYR cc_start: 0.8904 (t80) cc_final: 0.8555 (t80) REVERT: B 59 GLN cc_start: 0.8458 (tp40) cc_final: 0.8186 (tp-100) REVERT: C 62 GLU cc_start: 0.8795 (tp30) cc_final: 0.8565 (tp30) REVERT: C 186 ASN cc_start: 0.8805 (t0) cc_final: 0.8362 (t0) REVERT: D 16 ASP cc_start: 0.8426 (p0) cc_final: 0.8194 (p0) REVERT: D 62 GLU cc_start: 0.8669 (tp30) cc_final: 0.8151 (tp30) REVERT: D 125 TYR cc_start: 0.8823 (t80) cc_final: 0.7969 (t80) REVERT: E 163 ASP cc_start: 0.8137 (p0) cc_final: 0.7902 (p0) REVERT: E 172 ASN cc_start: 0.8661 (t0) cc_final: 0.8449 (t0) outliers start: 16 outliers final: 11 residues processed: 179 average time/residue: 0.0879 time to fit residues: 21.5528 Evaluate side-chains 158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN C 137 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 195 GLN E 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.079299 restraints weight = 12762.887| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.81 r_work: 0.2624 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8395 Z= 0.239 Angle : 0.556 4.280 11415 Z= 0.309 Chirality : 0.050 0.215 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.416 23.815 1100 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 12.22 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 1020 helix: 3.04 (0.68), residues: 55 sheet: -0.69 (0.32), residues: 280 loop : -1.20 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 6 TYR 0.017 0.002 TYR D 54 PHE 0.013 0.002 PHE A 180 TRP 0.007 0.001 TRP B 162 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 ( 8390) covalent geometry : angle 0.55549 / 0.31 (11405) SS BOND : bond 0.00276 / 0.15 ( 5) SS BOND : angle 0.90718 / 0.54 ( 10) hydrogen bonds : bond 0.04863 / 3.22 ( 290) hydrogen bonds : angle 5.30692 / 3.60 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.318 Fit side-chains REVERT: A 101 GLU cc_start: 0.8649 (tt0) cc_final: 0.8223 (tt0) REVERT: A 172 ASN cc_start: 0.8617 (t0) cc_final: 0.8400 (t0) REVERT: A 175 TYR cc_start: 0.8999 (t80) cc_final: 0.8676 (t80) REVERT: A 190 LEU cc_start: 0.9222 (tp) cc_final: 0.8834 (mp) REVERT: B 137 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8219 (mm-40) REVERT: D 62 GLU cc_start: 0.8966 (tp30) cc_final: 0.8425 (tp30) REVERT: D 125 TYR cc_start: 0.8836 (t80) cc_final: 0.8021 (t80) REVERT: D 163 ASP cc_start: 0.8293 (p0) cc_final: 0.8055 (p0) REVERT: E 49 TYR cc_start: 0.9132 (p90) cc_final: 0.8888 (p90) REVERT: E 163 ASP cc_start: 0.8291 (p0) cc_final: 0.8002 (p0) REVERT: E 172 ASN cc_start: 0.8692 (t0) cc_final: 0.8489 (t0) outliers start: 18 outliers final: 14 residues processed: 156 average time/residue: 0.0902 time to fit residues: 19.3696 Evaluate side-chains 155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 195 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN E 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.081447 restraints weight = 12648.154| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.83 r_work: 0.2687 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8395 Z= 0.138 Angle : 0.505 4.325 11415 Z= 0.281 Chirality : 0.048 0.172 1235 Planarity : 0.004 0.051 1450 Dihedral : 4.153 20.110 1100 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.89 % Allowed : 12.67 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.26), residues: 1020 helix: 3.19 (0.68), residues: 55 sheet: -0.87 (0.31), residues: 290 loop : -1.03 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 6 TYR 0.018 0.001 TYR B 54 PHE 0.010 0.001 PHE A 180 TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8390) covalent geometry : angle 0.50450 / 0.28 (11405) SS BOND : bond 0.00225 / 0.13 ( 5) SS BOND : angle 0.96245 / 0.57 ( 10) hydrogen bonds : bond 0.04226 / 2.78 ( 290) hydrogen bonds : angle 5.17508 / 3.54 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.283 Fit side-chains REVERT: A 101 GLU cc_start: 0.8603 (tt0) cc_final: 0.8143 (tt0) REVERT: A 147 GLU cc_start: 0.7609 (tt0) cc_final: 0.6942 (mt-10) REVERT: A 172 ASN cc_start: 0.8597 (t0) cc_final: 0.8386 (t0) REVERT: A 175 TYR cc_start: 0.8945 (t80) cc_final: 0.8682 (t80) REVERT: A 190 LEU cc_start: 0.9262 (tp) cc_final: 0.8843 (mp) REVERT: B 137 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8202 (mm-40) REVERT: B 190 LEU cc_start: 0.9205 (tp) cc_final: 0.8908 (mp) REVERT: C 175 TYR cc_start: 0.8944 (t80) cc_final: 0.8672 (t80) REVERT: D 62 GLU cc_start: 0.8856 (tp30) cc_final: 0.8321 (tp30) REVERT: D 125 TYR cc_start: 0.8802 (t80) cc_final: 0.7966 (t80) REVERT: D 163 ASP cc_start: 0.8246 (p0) cc_final: 0.8042 (p0) REVERT: E 85 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8491 (mp0) REVERT: E 163 ASP cc_start: 0.8203 (p0) cc_final: 0.7954 (p0) REVERT: E 172 ASN cc_start: 0.8642 (t0) cc_final: 0.8442 (t0) outliers start: 17 outliers final: 15 residues processed: 168 average time/residue: 0.0922 time to fit residues: 21.0838 Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 94 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN E 59 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.083112 restraints weight = 12485.013| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.82 r_work: 0.2686 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8395 Z= 0.100 Angle : 0.485 4.345 11415 Z= 0.269 Chirality : 0.048 0.176 1235 Planarity : 0.004 0.051 1450 Dihedral : 3.896 16.538 1100 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.00 % Allowed : 13.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 1020 helix: 3.25 (0.67), residues: 55 sheet: -0.77 (0.28), residues: 365 loop : -0.88 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 6 TYR 0.018 0.001 TYR B 54 PHE 0.009 0.001 PHE A 180 TRP 0.006 0.001 TRP B 162 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 8390) covalent geometry : angle 0.48445 / 0.27 (11405) SS BOND : bond 0.00485 / 0.28 ( 5) SS BOND : angle 0.96450 / 0.58 ( 10) hydrogen bonds : bond 0.03841 / 2.52 ( 290) hydrogen bonds : angle 5.04416 / 3.45 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.288 Fit side-chains REVERT: A 101 GLU cc_start: 0.8577 (tt0) cc_final: 0.8315 (tt0) REVERT: A 175 TYR cc_start: 0.8914 (t80) cc_final: 0.8625 (t80) REVERT: A 190 LEU cc_start: 0.9257 (tp) cc_final: 0.8813 (mp) REVERT: B 137 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8073 (mm-40) REVERT: B 190 LEU cc_start: 0.9223 (tp) cc_final: 0.8928 (mp) REVERT: C 175 TYR cc_start: 0.8899 (t80) cc_final: 0.8610 (t80) REVERT: D 62 GLU cc_start: 0.8836 (tp30) cc_final: 0.8324 (tp30) REVERT: D 125 TYR cc_start: 0.8802 (t80) cc_final: 0.7898 (t80) REVERT: D 163 ASP cc_start: 0.8169 (p0) cc_final: 0.7927 (p0) REVERT: D 190 LEU cc_start: 0.9171 (tp) cc_final: 0.8779 (mp) REVERT: E 83 LEU cc_start: 0.9265 (mm) cc_final: 0.8943 (mm) REVERT: E 163 ASP cc_start: 0.8207 (p0) cc_final: 0.7968 (p0) outliers start: 18 outliers final: 14 residues processed: 171 average time/residue: 0.0872 time to fit residues: 20.4515 Evaluate side-chains 168 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 195 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.077817 restraints weight = 12842.948| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.77 r_work: 0.2645 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 8395 Z= 0.312 Angle : 0.601 4.416 11415 Z= 0.333 Chirality : 0.052 0.193 1235 Planarity : 0.004 0.038 1450 Dihedral : 4.578 22.397 1100 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 13.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.26), residues: 1020 helix: 3.19 (0.66), residues: 55 sheet: -0.95 (0.26), residues: 395 loop : -1.04 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 118 TYR 0.023 0.002 TYR B 54 PHE 0.010 0.002 PHE E 52 TRP 0.008 0.001 TRP B 162 HIS 0.005 0.002 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.31 ( 8390) covalent geometry : angle 0.59937 / 0.33 (11405) SS BOND : bond 0.00629 / 0.36 ( 5) SS BOND : angle 1.38918 / 0.82 ( 10) hydrogen bonds : bond 0.04926 / 3.26 ( 290) hydrogen bonds : angle 5.23686 / 3.56 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.211 Fit side-chains REVERT: A 175 TYR cc_start: 0.9000 (t80) cc_final: 0.8702 (t80) REVERT: A 190 LEU cc_start: 0.9242 (tp) cc_final: 0.8826 (mp) REVERT: B 137 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8236 (mm-40) REVERT: D 62 GLU cc_start: 0.9014 (tp30) cc_final: 0.8553 (tp30) REVERT: D 125 TYR cc_start: 0.8847 (t80) cc_final: 0.8081 (t80) REVERT: E 163 ASP cc_start: 0.8311 (p0) cc_final: 0.8026 (p0) outliers start: 17 outliers final: 16 residues processed: 149 average time/residue: 0.0850 time to fit residues: 17.0948 Evaluate side-chains 155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN B 195 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.081259 restraints weight = 12605.532| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.81 r_work: 0.2663 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8395 Z= 0.128 Angle : 0.519 4.573 11415 Z= 0.289 Chirality : 0.049 0.178 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.157 18.524 1100 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.78 % Allowed : 14.44 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 1020 helix: 3.39 (0.68), residues: 55 sheet: -0.90 (0.26), residues: 395 loop : -0.95 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 6 TYR 0.021 0.001 TYR B 54 PHE 0.009 0.001 PHE E 33 TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8390) covalent geometry : angle 0.51845 / 0.29 (11405) SS BOND : bond 0.00209 / 0.12 ( 5) SS BOND : angle 1.14388 / 0.68 ( 10) hydrogen bonds : bond 0.04064 / 2.68 ( 290) hydrogen bonds : angle 5.11707 / 3.51 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.450 Fit side-chains REVERT: A 101 GLU cc_start: 0.8554 (tt0) cc_final: 0.8066 (tt0) REVERT: A 175 TYR cc_start: 0.8939 (t80) cc_final: 0.8663 (t80) REVERT: B 137 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8192 (mm-40) REVERT: B 190 LEU cc_start: 0.9228 (tp) cc_final: 0.8912 (mp) REVERT: C 175 TYR cc_start: 0.8930 (t80) cc_final: 0.8672 (t80) REVERT: D 62 GLU cc_start: 0.8862 (tp30) cc_final: 0.8351 (tp30) REVERT: D 125 TYR cc_start: 0.8819 (t80) cc_final: 0.7943 (t80) REVERT: E 83 LEU cc_start: 0.9217 (mm) cc_final: 0.8973 (mm) REVERT: E 163 ASP cc_start: 0.8249 (p0) cc_final: 0.7989 (p0) outliers start: 16 outliers final: 16 residues processed: 154 average time/residue: 0.0784 time to fit residues: 16.5815 Evaluate side-chains 154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.084698 restraints weight = 12573.023| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.78 r_work: 0.2711 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8395 Z= 0.107 Angle : 0.507 4.408 11415 Z= 0.281 Chirality : 0.048 0.186 1235 Planarity : 0.003 0.030 1450 Dihedral : 3.917 14.938 1100 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 14.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.27), residues: 1020 helix: 3.32 (0.67), residues: 55 sheet: -0.82 (0.27), residues: 395 loop : -0.83 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 6 TYR 0.022 0.001 TYR B 54 PHE 0.010 0.001 PHE A 33 TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8390) covalent geometry : angle 0.50624 / 0.28 (11405) SS BOND : bond 0.00390 / 0.23 ( 5) SS BOND : angle 1.13452 / 0.70 ( 10) hydrogen bonds : bond 0.03801 / 2.50 ( 290) hydrogen bonds : angle 5.03259 / 3.46 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.203 Fit side-chains REVERT: A 85 GLU cc_start: 0.8730 (mp0) cc_final: 0.8522 (mp0) REVERT: A 101 GLU cc_start: 0.8554 (tt0) cc_final: 0.8272 (tt0) REVERT: A 147 GLU cc_start: 0.7981 (tt0) cc_final: 0.7337 (mt-10) REVERT: A 175 TYR cc_start: 0.8896 (t80) cc_final: 0.8599 (t80) REVERT: A 190 LEU cc_start: 0.9227 (tp) cc_final: 0.8830 (mp) REVERT: B 137 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8068 (mm-40) REVERT: B 190 LEU cc_start: 0.9239 (tp) cc_final: 0.8952 (mp) REVERT: C 71 ILE cc_start: 0.8932 (mt) cc_final: 0.8701 (mt) REVERT: C 175 TYR cc_start: 0.8883 (t80) cc_final: 0.8615 (t80) REVERT: D 62 GLU cc_start: 0.8810 (tp30) cc_final: 0.8348 (tp30) REVERT: D 125 TYR cc_start: 0.8809 (t80) cc_final: 0.7919 (t80) REVERT: E 83 LEU cc_start: 0.9218 (mm) cc_final: 0.8982 (mm) REVERT: E 163 ASP cc_start: 0.8231 (p0) cc_final: 0.7977 (p0) outliers start: 16 outliers final: 15 residues processed: 168 average time/residue: 0.0728 time to fit residues: 16.8244 Evaluate side-chains 160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.082803 restraints weight = 12511.914| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.80 r_work: 0.2706 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8395 Z= 0.136 Angle : 0.522 4.736 11415 Z= 0.290 Chirality : 0.049 0.183 1235 Planarity : 0.004 0.030 1450 Dihedral : 3.994 15.724 1100 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.78 % Allowed : 15.00 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 1020 helix: 3.32 (0.68), residues: 55 sheet: -0.83 (0.27), residues: 395 loop : -0.82 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 6 TYR 0.023 0.002 TYR B 54 PHE 0.008 0.001 PHE E 52 TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8390) covalent geometry : angle 0.52060 / 0.29 (11405) SS BOND : bond 0.00347 / 0.20 ( 5) SS BOND : angle 1.19698 / 0.73 ( 10) hydrogen bonds : bond 0.03997 / 2.64 ( 290) hydrogen bonds : angle 5.00927 / 3.44 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.267 Fit side-chains REVERT: A 101 GLU cc_start: 0.8556 (tt0) cc_final: 0.8276 (tt0) REVERT: A 175 TYR cc_start: 0.8904 (t80) cc_final: 0.8592 (t80) REVERT: A 190 LEU cc_start: 0.9232 (tp) cc_final: 0.8823 (mp) REVERT: B 137 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8092 (mm-40) REVERT: B 190 LEU cc_start: 0.9229 (tp) cc_final: 0.8920 (mp) REVERT: C 175 TYR cc_start: 0.8892 (t80) cc_final: 0.8610 (t80) REVERT: D 62 GLU cc_start: 0.8860 (tp30) cc_final: 0.8406 (tp30) REVERT: D 125 TYR cc_start: 0.8824 (t80) cc_final: 0.7984 (t80) REVERT: E 83 LEU cc_start: 0.9227 (mm) cc_final: 0.8972 (mm) REVERT: E 163 ASP cc_start: 0.8264 (p0) cc_final: 0.7999 (p0) outliers start: 16 outliers final: 16 residues processed: 157 average time/residue: 0.0848 time to fit residues: 18.0804 Evaluate side-chains 161 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.083933 restraints weight = 12603.846| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.82 r_work: 0.2708 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8395 Z= 0.112 Angle : 0.508 5.895 11415 Z= 0.282 Chirality : 0.048 0.182 1235 Planarity : 0.003 0.030 1450 Dihedral : 3.894 14.349 1100 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.78 % Allowed : 15.22 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.27), residues: 1020 helix: 3.34 (0.67), residues: 55 sheet: -0.81 (0.27), residues: 395 loop : -0.77 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 6 TYR 0.023 0.001 TYR B 54 PHE 0.009 0.001 PHE A 33 TRP 0.008 0.001 TRP D 162 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 8390) covalent geometry : angle 0.50699 / 0.28 (11405) SS BOND : bond 0.00308 / 0.17 ( 5) SS BOND : angle 1.13624 / 0.70 ( 10) hydrogen bonds : bond 0.03797 / 2.50 ( 290) hydrogen bonds : angle 4.98356 / 3.43 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.11 seconds wall clock time: 26 minutes 6.23 seconds (1566.23 seconds total)