Starting phenix.real_space_refine on Mon Apr 28 23:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wv4_37864/04_2025/8wv4_37864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wv4_37864/04_2025/8wv4_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_37864/04_2025/8wv4_37864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wv4_37864/04_2025/8wv4_37864.map" model { file = "/net/cci-nas-00/data/ceres_data/8wv4_37864/04_2025/8wv4_37864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wv4_37864/04_2025/8wv4_37864.cif" } resolution = 3.3 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.57, per 1000 atoms: 0.44 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 C 36 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.05 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: 2.35 Time building geometry restraints manager: 2.10 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.330 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 (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: -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 TRP 0.003 0.000 TRP D 110 HIS 0.002 0.001 HIS D 38 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR A 54 ARG 0.008 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.28617 ( 290) hydrogen bonds : angle 8.32903 ( 735) SS BOND : bond 0.00039 ( 5) SS BOND : angle 0.02738 ( 10) covalent geometry : bond 0.00219 ( 8390) covalent geometry : angle 0.49079 (11405) *********************** 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 : 0.863 Fit side-chains REVERT: A 101 GLU cc_start: 0.8276 (tt0) cc_final: 0.7927 (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: 0.8556 (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: 0.1950 time to fit residues: 65.0602 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 : 0.886 ------------------------------------------------------------------------------- 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 84 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN B 195 GLN C 59 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.079409 restraints weight = 12604.374| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.74 r_work: 0.2579 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8395 Z= 0.299 Angle : 0.609 4.390 11415 Z= 0.340 Chirality : 0.052 0.167 1235 Planarity : 0.005 0.037 1450 Dihedral : 5.069 36.786 1108 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.78 % Allowed : 9.89 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.97 (0.25), residues: 1020 helix: 2.69 (0.67), residues: 55 sheet: -1.11 (0.25), residues: 390 loop : -1.89 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 205 HIS 0.007 0.002 HIS B 38 PHE 0.013 0.002 PHE C 109 TYR 0.021 0.002 TYR D 54 ARG 0.004 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 290) hydrogen bonds : angle 5.72591 ( 735) SS BOND : bond 0.00926 ( 5) SS BOND : angle 0.55404 ( 10) covalent geometry : bond 0.00719 ( 8390) covalent geometry : angle 0.60889 (11405) *********************** 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 170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.283 Fit side-chains REVERT: A 101 GLU cc_start: 0.8898 (tt0) cc_final: 0.8501 (tt0) REVERT: A 172 ASN cc_start: 0.8685 (t0) cc_final: 0.8472 (t0) REVERT: A 175 TYR cc_start: 0.9030 (t80) cc_final: 0.8716 (t80) REVERT: A 190 LEU cc_start: 0.9172 (tp) cc_final: 0.8813 (mp) REVERT: B 59 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7903 (tp-100) REVERT: B 137 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8388 (mm-40) REVERT: C 190 LEU cc_start: 0.9197 (tp) cc_final: 0.8843 (mp) REVERT: D 62 GLU cc_start: 0.8946 (tp30) cc_final: 0.8639 (tp30) REVERT: D 125 TYR cc_start: 0.8905 (t80) cc_final: 0.8026 (t80) REVERT: D 137 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8407 (mm-40) REVERT: D 193 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: E 49 TYR cc_start: 0.9227 (p90) cc_final: 0.8969 (p90) REVERT: E 163 ASP cc_start: 0.8441 (p0) cc_final: 0.8195 (p0) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.2112 time to fit residues: 47.8391 Evaluate side-chains 152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 59 GLN Chi-restraints excluded: chain B residue 76 THR 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 193 GLU Chi-restraints excluded: chain E residue 76 THR 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 24 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.082718 restraints weight = 12789.501| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.82 r_work: 0.2685 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2580 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= 0.105 Angle : 0.499 4.138 11415 Z= 0.278 Chirality : 0.048 0.163 1235 Planarity : 0.003 0.030 1450 Dihedral : 4.050 18.447 1100 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.89 % Allowed : 11.22 % Favored : 87.89 % 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: -1.41 (0.25), residues: 1020 helix: 2.97 (0.69), residues: 55 sheet: -0.76 (0.32), residues: 280 loop : -1.41 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.002 0.001 HIS E 38 PHE 0.009 0.001 PHE B 109 TYR 0.014 0.001 TYR B 54 ARG 0.003 0.000 ARG C 6 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 290) hydrogen bonds : angle 5.38018 ( 735) SS BOND : bond 0.00502 ( 5) SS BOND : angle 0.65425 ( 10) covalent geometry : bond 0.00246 ( 8390) covalent geometry : angle 0.49930 (11405) *********************** 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 170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.924 Fit side-chains REVERT: A 101 GLU cc_start: 0.8613 (tt0) cc_final: 0.8206 (tt0) REVERT: A 175 TYR cc_start: 0.8926 (t80) cc_final: 0.8660 (t80) REVERT: A 190 LEU cc_start: 0.9202 (tp) cc_final: 0.8868 (mp) REVERT: B 137 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 62 GLU cc_start: 0.8764 (tp30) cc_final: 0.8547 (tp30) REVERT: C 190 LEU cc_start: 0.9177 (tp) cc_final: 0.8908 (mp) REVERT: D 16 ASP cc_start: 0.8514 (p0) cc_final: 0.8257 (p0) REVERT: D 62 GLU cc_start: 0.8664 (tp30) cc_final: 0.8156 (tp30) REVERT: D 125 TYR cc_start: 0.8820 (t80) cc_final: 0.7878 (t80) REVERT: E 163 ASP cc_start: 0.8180 (p0) cc_final: 0.7949 (p0) REVERT: E 180 PHE cc_start: 0.8352 (p90) cc_final: 0.7981 (p90) outliers start: 8 outliers final: 4 residues processed: 168 average time/residue: 0.2119 time to fit residues: 48.1889 Evaluate side-chains 150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 139 GLN Chi-restraints excluded: chain B residue 169 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN B 150 GLN B 195 GLN C 195 GLN D 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.080480 restraints weight = 12740.085| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.76 r_work: 0.2605 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8395 Z= 0.216 Angle : 0.542 4.208 11415 Z= 0.303 Chirality : 0.050 0.234 1235 Planarity : 0.004 0.055 1450 Dihedral : 4.318 22.373 1100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.67 % Allowed : 11.44 % Favored : 86.89 % 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: -1.21 (0.25), residues: 1020 helix: 2.99 (0.68), residues: 55 sheet: -0.69 (0.32), residues: 280 loop : -1.22 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.002 PHE A 66 TYR 0.017 0.002 TYR B 54 ARG 0.003 0.001 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 290) hydrogen bonds : angle 5.31222 ( 735) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.80752 ( 10) covalent geometry : bond 0.00522 ( 8390) covalent geometry : angle 0.54211 (11405) *********************** 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 163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.959 Fit side-chains REVERT: A 101 GLU cc_start: 0.8781 (tt0) cc_final: 0.8374 (tt0) REVERT: A 175 TYR cc_start: 0.9015 (t80) cc_final: 0.8670 (t80) REVERT: A 190 LEU cc_start: 0.9258 (tp) cc_final: 0.8824 (mp) REVERT: B 137 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8288 (mm-40) REVERT: B 190 LEU cc_start: 0.9221 (tp) cc_final: 0.8897 (mp) REVERT: C 190 LEU cc_start: 0.9218 (tp) cc_final: 0.8825 (mp) REVERT: D 16 ASP cc_start: 0.8597 (p0) cc_final: 0.8373 (p0) REVERT: D 62 GLU cc_start: 0.9064 (tp30) cc_final: 0.8570 (tp30) REVERT: D 125 TYR cc_start: 0.8878 (t80) cc_final: 0.8067 (t80) REVERT: E 49 TYR cc_start: 0.9208 (p90) cc_final: 0.8965 (p90) REVERT: E 163 ASP cc_start: 0.8414 (p0) cc_final: 0.8142 (p0) outliers start: 15 outliers final: 13 residues processed: 159 average time/residue: 0.2492 time to fit residues: 53.1570 Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 94 VAL 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 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 7 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 195 GLN D 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.080311 restraints weight = 12727.617| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.75 r_work: 0.2574 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2958 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= 0.206 Angle : 0.536 4.243 11415 Z= 0.300 Chirality : 0.049 0.199 1235 Planarity : 0.004 0.052 1450 Dihedral : 4.359 21.080 1100 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.11 % Allowed : 11.78 % Favored : 86.11 % 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: -1.16 (0.26), residues: 1020 helix: 3.11 (0.68), residues: 55 sheet: -0.86 (0.31), residues: 290 loop : -1.09 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.003 0.001 HIS D 38 PHE 0.008 0.002 PHE C 39 TYR 0.018 0.002 TYR B 54 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 290) hydrogen bonds : angle 5.26204 ( 735) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.09423 ( 10) covalent geometry : bond 0.00496 ( 8390) covalent geometry : angle 0.53522 (11405) *********************** 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 165 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.893 Fit side-chains REVERT: A 101 GLU cc_start: 0.8755 (tt0) cc_final: 0.8326 (tt0) REVERT: A 175 TYR cc_start: 0.9014 (t80) cc_final: 0.8681 (t80) REVERT: A 190 LEU cc_start: 0.9264 (tp) cc_final: 0.8812 (mp) REVERT: B 137 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8326 (mm-40) REVERT: B 190 LEU cc_start: 0.9237 (tp) cc_final: 0.8847 (mp) REVERT: C 190 LEU cc_start: 0.9307 (tp) cc_final: 0.8896 (mp) REVERT: D 16 ASP cc_start: 0.8576 (p0) cc_final: 0.8363 (p0) REVERT: D 62 GLU cc_start: 0.9084 (tp30) cc_final: 0.8628 (tp30) REVERT: D 125 TYR cc_start: 0.8896 (t80) cc_final: 0.8012 (t80) REVERT: E 49 TYR cc_start: 0.9212 (p90) cc_final: 0.8905 (p90) REVERT: E 163 ASP cc_start: 0.8350 (p0) cc_final: 0.8077 (p0) outliers start: 19 outliers final: 17 residues processed: 160 average time/residue: 0.2318 time to fit residues: 50.2610 Evaluate side-chains 159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 94 VAL 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 38 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 195 GLN D 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.080608 restraints weight = 12651.520| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.70 r_work: 0.2656 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8395 Z= 0.162 Angle : 0.515 4.327 11415 Z= 0.288 Chirality : 0.049 0.175 1235 Planarity : 0.004 0.037 1450 Dihedral : 4.232 19.725 1100 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.00 % Allowed : 12.44 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.26), residues: 1020 helix: 3.19 (0.68), residues: 55 sheet: -0.96 (0.26), residues: 395 loop : -1.02 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE C 39 TYR 0.019 0.001 TYR B 54 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 290) hydrogen bonds : angle 5.20080 ( 735) SS BOND : bond 0.00349 ( 5) SS BOND : angle 1.06622 ( 10) covalent geometry : bond 0.00388 ( 8390) covalent geometry : angle 0.51472 (11405) *********************** 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 166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.979 Fit side-chains REVERT: A 101 GLU cc_start: 0.8708 (tt0) cc_final: 0.8269 (tt0) REVERT: A 175 TYR cc_start: 0.8993 (t80) cc_final: 0.8730 (t80) REVERT: B 137 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8282 (mm-40) REVERT: B 190 LEU cc_start: 0.9262 (tp) cc_final: 0.8891 (mp) REVERT: D 62 GLU cc_start: 0.9048 (tp30) cc_final: 0.8595 (tp30) REVERT: D 125 TYR cc_start: 0.8884 (t80) cc_final: 0.8001 (t80) REVERT: E 83 LEU cc_start: 0.9315 (mm) cc_final: 0.9058 (mm) REVERT: E 163 ASP cc_start: 0.8346 (p0) cc_final: 0.8082 (p0) outliers start: 18 outliers final: 16 residues processed: 161 average time/residue: 0.3139 time to fit residues: 68.4903 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 : 1.506 ------------------------------------------------------------------------------- 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 53 SER 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 38 HIS 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 67 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN D 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.079466 restraints weight = 12730.907| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.65 r_work: 0.2655 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8395 Z= 0.229 Angle : 0.554 4.474 11415 Z= 0.309 Chirality : 0.050 0.186 1235 Planarity : 0.004 0.032 1450 Dihedral : 4.427 21.512 1100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 12.00 % 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 (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: -1.21 (0.26), residues: 1020 helix: 3.17 (0.67), residues: 55 sheet: -0.95 (0.26), residues: 395 loop : -1.05 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.002 PHE E 52 TYR 0.020 0.002 TYR B 54 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 290) hydrogen bonds : angle 5.25254 ( 735) SS BOND : bond 0.00373 ( 5) SS BOND : angle 1.26390 ( 10) covalent geometry : bond 0.00550 ( 8390) covalent geometry : angle 0.55286 (11405) *********************** 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 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.014 Fit side-chains REVERT: A 101 GLU cc_start: 0.8723 (tt0) cc_final: 0.8438 (tt0) REVERT: A 175 TYR cc_start: 0.9010 (t80) cc_final: 0.8743 (t80) REVERT: B 38 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8333 (t70) REVERT: B 137 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8316 (mm-40) REVERT: B 190 LEU cc_start: 0.9271 (tp) cc_final: 0.8901 (mp) REVERT: D 62 GLU cc_start: 0.9091 (tp30) cc_final: 0.8665 (tp30) REVERT: D 125 TYR cc_start: 0.8902 (t80) cc_final: 0.8041 (t80) REVERT: E 163 ASP cc_start: 0.8363 (p0) cc_final: 0.8104 (p0) outliers start: 23 outliers final: 21 residues processed: 159 average time/residue: 0.2138 time to fit residues: 46.0493 Evaluate side-chains 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 38 HIS 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 38 HIS 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 38 HIS 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 58 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3113 r_free = 0.3113 target = 0.100182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.081146 restraints weight = 12913.454| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.80 r_work: 0.2615 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8395 Z= 0.156 Angle : 0.525 4.688 11415 Z= 0.294 Chirality : 0.049 0.180 1235 Planarity : 0.004 0.032 1450 Dihedral : 4.230 19.363 1100 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.33 % Allowed : 12.78 % Favored : 84.89 % 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: -1.14 (0.27), residues: 1020 helix: 3.24 (0.68), residues: 55 sheet: -0.92 (0.27), residues: 395 loop : -0.98 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS E 38 PHE 0.008 0.001 PHE E 52 TYR 0.021 0.001 TYR B 54 ARG 0.001 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 290) hydrogen bonds : angle 5.19132 ( 735) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.25220 ( 10) covalent geometry : bond 0.00375 ( 8390) covalent geometry : angle 0.52433 (11405) *********************** 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 167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.955 Fit side-chains REVERT: A 101 GLU cc_start: 0.8549 (tt0) cc_final: 0.8278 (tt0) REVERT: A 175 TYR cc_start: 0.8956 (t80) cc_final: 0.8686 (t80) REVERT: B 38 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8157 (t70) REVERT: B 137 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8142 (mm-40) REVERT: B 190 LEU cc_start: 0.9241 (tp) cc_final: 0.8906 (mp) REVERT: D 62 GLU cc_start: 0.8935 (tp30) cc_final: 0.8476 (tp30) REVERT: D 125 TYR cc_start: 0.8835 (t80) cc_final: 0.7956 (t80) REVERT: E 83 LEU cc_start: 0.9288 (mm) cc_final: 0.9044 (mm) REVERT: E 163 ASP cc_start: 0.8215 (p0) cc_final: 0.7954 (p0) outliers start: 21 outliers final: 20 residues processed: 162 average time/residue: 0.2066 time to fit residues: 45.3667 Evaluate side-chains 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 53 SER 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 38 HIS 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 38 HIS 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 38 HIS 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 50 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3115 r_free = 0.3115 target = 0.100207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.081803 restraints weight = 12937.760| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.73 r_work: 0.2681 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8395 Z= 0.148 Angle : 0.526 4.519 11415 Z= 0.294 Chirality : 0.049 0.180 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.154 17.946 1100 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.33 % Allowed : 12.89 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.09 (0.27), residues: 1020 helix: 3.25 (0.68), residues: 55 sheet: -0.88 (0.27), residues: 395 loop : -0.96 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS E 38 PHE 0.009 0.001 PHE E 52 TYR 0.021 0.001 TYR B 54 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 290) hydrogen bonds : angle 5.16638 ( 735) SS BOND : bond 0.00398 ( 5) SS BOND : angle 1.26178 ( 10) covalent geometry : bond 0.00356 ( 8390) covalent geometry : angle 0.52488 (11405) *********************** 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 171 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8684 (tt0) cc_final: 0.8417 (tt0) REVERT: A 175 TYR cc_start: 0.8984 (t80) cc_final: 0.8709 (t80) REVERT: B 38 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8298 (t70) REVERT: B 137 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8220 (mm-40) REVERT: B 190 LEU cc_start: 0.9274 (tp) cc_final: 0.8900 (mp) REVERT: D 62 GLU cc_start: 0.9038 (tp30) cc_final: 0.8578 (tp30) REVERT: D 125 TYR cc_start: 0.8865 (t80) cc_final: 0.7953 (t80) REVERT: E 83 LEU cc_start: 0.9324 (mm) cc_final: 0.8963 (mm) REVERT: E 163 ASP cc_start: 0.8334 (p0) cc_final: 0.8056 (p0) outliers start: 21 outliers final: 20 residues processed: 165 average time/residue: 0.2080 time to fit residues: 46.6962 Evaluate side-chains 166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 53 SER 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 38 HIS 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 38 HIS 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 38 HIS 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 60 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 0.0170 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3096 r_free = 0.3096 target = 0.098991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.080024 restraints weight = 12715.398| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.76 r_work: 0.2561 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8395 Z= 0.234 Angle : 0.579 5.352 11415 Z= 0.323 Chirality : 0.051 0.186 1235 Planarity : 0.004 0.031 1450 Dihedral : 4.429 20.733 1100 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.33 % Allowed : 13.11 % 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 (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: -1.19 (0.26), residues: 1020 helix: 3.22 (0.67), residues: 55 sheet: -0.73 (0.26), residues: 430 loop : -1.24 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.004 0.001 HIS D 38 PHE 0.009 0.002 PHE E 52 TYR 0.024 0.002 TYR B 54 ARG 0.002 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 290) hydrogen bonds : angle 5.25797 ( 735) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.45909 ( 10) covalent geometry : bond 0.00565 ( 8390) covalent geometry : angle 0.57743 (11405) ********************** 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 160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.889 Fit side-chains REVERT: A 101 GLU cc_start: 0.8729 (tt0) cc_final: 0.8425 (tt0) REVERT: A 175 TYR cc_start: 0.8978 (t80) cc_final: 0.8705 (t80) REVERT: B 38 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8254 (t70) REVERT: B 137 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8304 (mm-40) REVERT: D 62 GLU cc_start: 0.9095 (tp30) cc_final: 0.8659 (tp30) REVERT: D 125 TYR cc_start: 0.8879 (t80) cc_final: 0.7963 (t80) REVERT: E 163 ASP cc_start: 0.8346 (p0) cc_final: 0.8076 (p0) outliers start: 21 outliers final: 20 residues processed: 155 average time/residue: 0.2092 time to fit residues: 43.8914 Evaluate side-chains 160 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 53 SER 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 38 HIS 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 38 HIS 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 38 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.3980 chunk 94 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3142 r_free = 0.3142 target = 0.101934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.082886 restraints weight = 12747.525| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.81 r_work: 0.2714 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3205 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= 0.112 Angle : 0.527 5.774 11415 Z= 0.293 Chirality : 0.048 0.178 1235 Planarity : 0.003 0.031 1450 Dihedral : 4.026 15.772 1100 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 13.44 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.06 (0.27), residues: 1020 helix: 3.23 (0.68), residues: 55 sheet: -0.69 (0.26), residues: 430 loop : -1.10 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.004 0.001 HIS E 38 PHE 0.010 0.001 PHE A 33 TYR 0.022 0.001 TYR B 54 ARG 0.002 0.000 ARG E 6 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 290) hydrogen bonds : angle 5.12375 ( 735) SS BOND : bond 0.00409 ( 5) SS BOND : angle 1.21863 ( 10) covalent geometry : bond 0.00267 ( 8390) covalent geometry : angle 0.52608 (11405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.14 seconds wall clock time: 71 minutes 23.45 seconds (4283.45 seconds total)